YASARA Homology Modeling Report for HOMOLOGY

1. The homology modeling target HOMOLOGY

The three-dimensional structure of the following target sequence has been predicted by YASARA's homology modeling experiment, Version 22.5.22.W.64:

>HOMOLOGY
MDQSNRYANLNLKEEDLIKNGKHLLVAYKLIPAKGHGFLEVAAHVAAESSTGTNVEVSTT
DDFTRGVDALVYEIDETAFGDDPVKGGGLFKVAYPVELFDPNLTDGTYNISHMWSLILGN
NQGMGDHQGLRMLDFLVPEMMVRKFDGPSANISNLWKVLGRSETDGGYIAGTIIKPKLGL
RPEPFAKACYDFWLGGDFIKNDEPQANQPFCPMEVVMPKVAEAMDRAQQATGQAKLFSAN
ITADYYKEMIHRGDFVLETFAKYNSASHVAFLVDGFVTGPAGVTTARREFPDTFLHFHRA
GHGAVTSYKSPMGMDPLCYMKLVRLMGASGMHTGTMGYGKMEGHGKETVLAYMLERDECQ
GPYFYQKWYGMKATTPIISGGMNALRLPGFFQNLGHGNVINTCGGGAFGHIDSPAAGGIS
LGQAYDCWKSGSDPIEYAKTHKEFARAFESFPKDGDKLFAGWREKLGVHK

The target sequence contains 470 residues in 1 molecule.

2. The homology modeling parameters

The following parameters have been chosen for this target:

3. The homology modeling templates

Since the target sequence was the only available information, possible templates were identified by running 3 PSI-BLAST iterations to extract a position specific scoring matrix (PSSM) from UniRef90, and then searching the PDB for a match (i.e. hits with an E-value below the homology modeling cutoff 0.1).

The following 75 hits were found:

TemplateTotal scoreBLAST E-valueAlign scoreCoverIDResolutionHeader
11591.16 6e-0891989.096%7T1C-A1.73 AXRAY Ribulose bisphosphate carboxylase [Sulfurivirga caldicuralii] <A0A1N6DK16_9GAMM(1-466)> (453 residues with quality score 0.830), released 2022-09-07
21397.87 5e-0991687.095%5C2C-A2.09 AXRAY Ribulose-bisphosphate carboxylase [Gallionella] <A0A0X1KHE5_9PROT(1-459)> (448 residues with quality score 0.875), released 2015-12-16
31333.87 9e-0901566.097%5HQM-A1.95 AXRAY Ribulose bisphosphate carboxylase [Rhodospirillum rubrum] <RBL2_RHORU(456-466)> (459 residues with quality score 0.876), released 2017-01-25
41316.91 7e-0901560.097%5HAN-A2.04 AXRAY Ribulose bisphosphate carboxylase [Rhodopseudomonas palustris] <RBL2_RHOPA(1-461)> (456 residues with quality score 0.872), released 2017-01-04
51311.34 2e-0891564.097%5HJX-B1.80 AXRAY Ribulose bisphosphate carboxylase [Rhodopseudomonas palustris] <RBL2_RHOPA(1-461)> (455 residues with quality score 0.868), released 2017-01-18
-1307.47 1e-0891554.097%5HAT-J-XRAY Ribulose bisphosphate carboxylase [Rhodopseudomonas palustris] <RBL2_RHOPA(1-461)> (455 residues with quality score 0.871), released 2017-01-04. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-1299.77 1e-0891563.097%5KOZ-D-XRAY Ribulose bisphosphate carboxylase [Rhodopseudomonas palustris] <RBL2_RHOPA(1-461)> (456 residues with quality score 0.859), released 2017-07-05. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-1296.92 6e-0901563.097%5HJY-A-XRAY Ribulose bisphosphate carboxylase [Rhodopseudomonas palustris] <RBL2_RHOPA(1-461)> (455 residues with quality score 0.859), released 2017-01-18. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-1294.27 4e-0891558.097%5HAO-A-XRAY Ribulose bisphosphate carboxylase [Rhodopseudomonas palustris] <RBL2_RHOPA(1-461)> (455 residues with quality score 0.860), released 2017-01-04. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-1290.75 2e-0891556.097%5HQL-B-XRAY Ribulose bisphosphate carboxylase [Rhodopseudomonas palustris] <RBL2_RHOPA(1-461)> (457 residues with quality score 0.855), released 2017-01-25. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-1265.62 4e-0901566.097%4LF2-D-XRAY Ribulose bisphosphate carboxylase [Rhodopseudomonas palustris] <RBL2_RHOPA(1-461)> (457 residues with quality score 0.833), released 2014-06-25. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-1223.09 6e-0951537.097%7T1J-A-XRAY Ribulose bisphosphate carboxylase [Rhodospirillaceae bacterium BRH_c57] <A0A0F2R9T6_9PROT(1-460)> (455 residues with quality score 0.822), released 2022-09-07. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-1070.68 3e-0821484.091%6IUS-A-XRAY Ribulose-bisphosphate carboxylase [endosymbiont of Riftia pachyptila] <O68486_9GAMM(1-461)> (426 residues with quality score 0.796), released 2019-12-04. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-1047.48 4e-0931544.092%5RUB-B-XRAY Ribulose bisphosphate carboxylase [Rhodospirillum rubrum] <RBL2_RHORU(1-466)> (433 residues with quality score 0.738), released 1991-10-15. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-554.93 1e-055790.092%5MAC-B-XRAY Ribulose-1,5-bisphosphate carboxylase-oxygenase type III [Methanococcoides burtonii] <Q12TQ0_METBU(1-474)> (473 residues with quality score 0.766), released 2017-02-08. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-386.37 6e-0861464.094%1RBA-B-XRAY Ribulose bisphosphate carboxylase [Rhodospirillum rubrum] <RBL2_RHORU(1-466)> (443 residues with quality score 0.280), released 1994-01-31. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-371.44 4e-066499.089%6HUN-A-XRAY Ribulose bisphosphate carboxylase [Hyperthermus butylicus] <A2BK54_HYPBU(1-441)> (428 residues with quality score 0.841), released 2019-06-12. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-352.97 4e-062473.089%3KDN-D-XRAY Ribulose bisphosphate carboxylase [Thermococcus kodakarensis] <RBL_THEKO(1-444)> (437 residues with quality score 0.841), released 2010-10-06. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-344.94 2e-062470.088%3A12-I-XRAY Ribulose bisphosphate carboxylase [Thermococcus kodakarensis] <RBL_THEKO(1-444)> (436 residues with quality score 0.831), released 2010-04-07. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-343.79 3e-062464.089%3WQP-A-XRAY Ribulose bisphosphate carboxylase [Thermococcus kodakarensis] <RBL_THEKO(1-444)> (437 residues with quality score 0.837), released 2015-02-04. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-338.76 3e-062470.088%3KDO-D-XRAY Ribulose bisphosphate carboxylase [Thermococcus kodakarensis] <RBL_THEKO(1-444)> (437 residues with quality score 0.816), released 2010-10-06. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-289.85 6e-107374.089%6KYJ-G-XRAY Ribulose bisphosphate carboxylase large chain [Oryza sativa] <RBL_ORYSJ(1-477)> (447 residues with quality score 0.871), released 2020-09-16. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-288.26 6e-108372.090%1WDD-A-XRAY Ribulose bisphosphate carboxylase large chain [Oryza sativa] <RBL_ORYSJ(1-477)> (465 residues with quality score 0.861), released 2004-11-13. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-282.96 4e-092348.091%1SVD-A-XRAY Ribulose bisphosphate carboxylase large chain [Halothiobacillus neapolitanus] <RBL1_HALNC(1-473)> (445 residues with quality score 0.895), released 2005-04-12. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-279.02 2e-105366.090%5WSK-D-XRAY Ribulose bisphosphate carboxylase large chain [Triticum aestivum] <RBL_WHEAT(1-477)> (440 residues with quality score 0.851), released 2018-02-14. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-278.20 6e-064377.090%6URA-B-XRAY Ribulose bisphosphate carboxylase large chain [Candidatus Promineofilum breve] <A0A160T9D2_9CHLR(1-463)> (440 residues with quality score 0.816), released 2020-08-19. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-277.84 7e-106366.092%3ZXW-G-XRAY Ribulose bisphosphate carboxylase large chain [Thermosynechococcus elongatus] <RBL_THEEB(1-475)> (464 residues with quality score 0.824), released 2012-08-29. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-274.06 3e-109366.090%4MKV-B-XRAY Ribulose bisphosphate carboxylase large chain [Pisum sativum] <RBL_PEA(12-469)> (458 residues with quality score 0.832), released 2013-10-16. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-272.93 9e-110370.093%1EJ7-L-XRAY Ribulose bisphosphate carboxylase large chain [Nicotiana tabacum] <RBL_TOBAC(3-477)> (457 residues with quality score 0.797), released 2000-03-15. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-268.43 8e-105350.091%2V6A-D-XRAY Ribulose bisphosphate carboxylase large chain [Chlamydomonas reinhardtii] <RBL_CHLRE(1-475)> (466 residues with quality score 0.844), released 2007-07-31. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-267.41 7e-105350.091%1GK8-A-XRAY Ribulose bisphosphate carboxylase large chain [Chlamydomonas reinhardtii] <RBL_CHLRE(1-475)> (469 residues with quality score 0.839), released 2001-10-24. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-265.38 4e-107355.091%1RBO-L-XRAY Ribulose bisphosphate carboxylase large chain [Spinacia oleracea] <RBL_SPIOL(1-475)> (467 residues with quality score 0.819), released 1997-03-12. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-264.14 8e-105353.090%2V67-A-XRAY Ribulose bisphosphate carboxylase large chain [Chlamydomonas reinhardtii] <RBL_CHLRE(1-475)> (466 residues with quality score 0.827), released 2007-08-07. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-263.81 3e-105352.091%1UW9-H-XRAY Ribulose bisphosphate carboxylase large chain [Chlamydomonas reinhardtii] <RBL_CHLRE(1-475)> (469 residues with quality score 0.823), released 2005-01-12. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-263.77 1e-108354.090%5IU0-A-XRAY Ribulose bisphosphate carboxylase large chain [Arabidopsis thaliana] <RBL_ARATH(1-479)> (463 residues with quality score 0.824), released 2017-07-12. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-263.56 2e-106350.091%8RUC-C-XRAY Ribulose bisphosphate carboxylase large chain [Spinacia oleracea] <RBL_SPIOL(1-475)> (467 residues with quality score 0.825), released 1996-08-01. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-262.92 1e-104352.091%2V68-A-XRAY Ribulose bisphosphate carboxylase large chain [Chlamydomonas reinhardtii] <RBL_CHLRE(1-475)> (466 residues with quality score 0.822), released 2007-08-07. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-260.38 2e-057367.086%2D69-B-XRAY Ribulose bisphosphate carboxylase [Pyrococcus horikoshii] <RBL_PYRHO(1-430)> (418 residues with quality score 0.827), released 2006-05-10. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-259.70 5e-095374.087%2YBV-E-XRAY Ribulose bisphosphate carboxylase large chain [Thermosynechococcus elongatus] <RBL_THEEB(1-475)> (428 residues with quality score 0.796), released 2012-03-28. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-259.27 2e-104345.090%2V63-A-XRAY Ribulose bisphosphate carboxylase large chain [Chlamydomonas reinhardtii] <RBL_CHLRE(1-475)> (466 residues with quality score 0.835), released 2007-07-31. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-259.18 2e-097351.093%1BWV-C-XRAY Ribulose bisphosphate carboxylase large chain [Galdieria partita] <O98949_9RHOD(1-493)> (472 residues with quality score 0.796), released 1999-09-27. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-259.07 5e-105356.090%1UWA-R-XRAY Ribulose bisphosphate carboxylase large chain [Chlamydomonas reinhardtii] <RBL_CHLRE(1-475)> (465 residues with quality score 0.806), released 2005-01-12. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-258.93 1e-104352.090%2VDH-A-XRAY Ribulose bisphosphate carboxylase large chain [Chlamydomonas reinhardtii] <RBL_CHLRE(1-475)> (465 residues with quality score 0.813), released 2008-11-04. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-258.72 2e-061459.088%1GEH-B-XRAY Ribulose bisphosphate carboxylase [Thermococcus kodakarensis] <RBL_THEKO(1-444)> (427 residues with quality score 0.643), released 2001-12-19. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-258.60 2e-103375.088%7JSX-K-XRAY Ribulose bisphosphate carboxylase large chain [Chlamydomonas reinhardtii] <RBL_CHLRE(1-475)> (444 residues with quality score 0.781), released 2020-11-18. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-257.73 4e-106360.091%1RBL-H-XRAY Ribulose bisphosphate carboxylase large chain [Synechococcus sp.] <RBL_SYNP6(6-472)> (467 residues with quality score 0.788), released 1994-06-22. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-257.50 1e-104369.091%6KKM-A-XRAY Ribulose bisphosphate carboxylase large chain [Nostoc sp.] <RBL_NOSS1(1-476)> (451 residues with quality score 0.768), released 2020-05-13. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-254.29 8e-105350.090%2VDI-A-XRAY Ribulose bisphosphate carboxylase large chain [Chlamydomonas reinhardtii] <RBL_CHLRE(1-475)> (465 residues with quality score 0.803), released 2008-11-04. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-254.09 5e-106362.086%6HBC-C-XRAY Ribulose bisphosphate carboxylase large chain [Synechococcus sp.] <RBL_SYNP6(1-472)> (440 residues with quality score 0.820), released 2018-12-12. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-251.85 2e-105355.090%1RXO-L-XRAY Ribulose bisphosphate carboxylase large chain [Spinacia oleracea] <RBL_SPIOL(1-475)> (455 residues with quality score 0.792), released 1997-06-16. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-247.98 1e-094362.092%4F0H-A-XRAY Ribulose bisphosphate carboxylase large chain [Galdieria sulphuraria] <RBL_GALSU(1-493)> (448 residues with quality score 0.747), released 2012-11-14. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-246.19 2e-091339.091%6UEW-A-XRAY Ribulose bisphosphate carboxylase large chain [Halothiobacillus neapolitanus] <RBL1_HALNC(2-473)> (453 residues with quality score 0.801), released 2019-10-30. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-242.08 7e-103356.091%3RUB-L-XRAY Ribulose bisphosphate carboxylase large chain [Nicotiana tabacum] <RBL_TOBAC(1-477)> (441 residues with quality score 0.745), released 1992-10-15. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-239.10 3e-098356.093%1IWA-C-XRAY Ribulose bisphosphate carboxylase large chain [Galdieria partita] <O98949_9RHOD(1-493)> (473 residues with quality score 0.724), released 2003-04-30. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-227.83 6e-103355.092%6Z1F-A-EM Ribulose bisphosphate carboxylase large chain [Nostoc sp.] <RBL_NOSS1(1-476)> (466 residues with quality score 0.695), released 2020-09-23. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-215.04 9e-089276.093%5MZ2-G-XRAY Ribulose bisphosphate carboxylase large chain (Fragment) [Thalassiosira antarctica] <A8DP67_9STRA(1-490)> (481 residues with quality score 0.834), released 2018-02-14. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-214.97 1e-088276.094%5N9Z-C-XRAY Ribulose-bisphosphate carboxylase [Thalassiosira hyalina] <A0A384E0M2_9STRA(1-490)> (481 residues with quality score 0.832), released 2018-03-14. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-213.78 4e-109366.088%1RLC-L-XRAY Ribulose bisphosphate carboxylase large chain [Nicotiana tabacum] <RBL_TOBAC(1-477)> (441 residues with quality score 0.664), released 1993-10-31. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-213.15 4e-088278.094%5OYA-C-XRAY Ribulose-bisphosphate carboxylase [Chaetoceros socialis] <A0A3B6UEF4_9STRA(1-490)> (468 residues with quality score 0.819), released 2018-06-27. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-210.86 3e-094331.089%1BXN-G-XRAY Ribulose bisphosphate carboxylase large chain, chromosomal [Cupriavidus necator] <RBL1C_CUPNE(1-486)> (445 residues with quality score 0.718), released 1999-10-06. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-203.61 2e-089282.093%6FTL-G-XRAY Ribulose-bisphosphate carboxylase [Skeletonema marinoi] <A0A3B6UEX0_9STRA(1-484)> (482 residues with quality score 0.773), released 2018-06-27. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-197.59 1e-103362.091%1RLD-A-XRAY Ribulose bisphosphate carboxylase large chain [Nicotiana tabacum] <RBL_TOBAC(22-467)> (441 residues with quality score 0.598), released 1994-04-30. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-197.46 9e-087334.090%7ZC1-P-EM Ribulose bisphosphate carboxylase large chain [Cyanobium sp. PCC 7001] <A5CKD0_9CYAN(1-470)> (445 residues with quality score 0.660), released 2022-07-06. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-195.40 9e-096302.094%5NV3-D-EM Ribulose bisphosphate carboxylase large chain [Rhodobacter sphaeroides] <RBL1_RHOSH(13-479)> (467 residues with quality score 0.688), released 2017-07-26. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-181.89 2e-102367.090%6SMH-A-EM Ribulose bisphosphate carboxylase large chain [Synechococcus elongatus] <RBL_SYNE7(19-465)> (447 residues with quality score 0.552), released 2020-07-08. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-158.88 2e-043243.084%1YKW-A-XRAY Ribulose bisphosphate carboxylase-like protein [Chlorobaculum tepidum] <RBLL_CHLTE(1-435)> (414 residues with quality score 0.776), released 2005-05-17. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-156.52 2e-049250.087%1TEL-B-XRAY Ribulose bisphosphate carboxylase-like protein [Chlorobaculum tepidum] <RBLL_CHLTE(1-435)> (428 residues with quality score 0.723), released 2004-10-05. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-142.04 9e-048247.085%2QYG-B-XRAY Ribulose bisphosphate carboxylase-like protein 2 [Rhodopseudomonas palustris] <RBLL2_RHOPA(1-432)> (429 residues with quality score 0.674), released 2007-09-11. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-140.94 3e-038201.082%3NWR-A-XRAY A rubisco-like protein [Paraburkholderia fungorum] <D9N172_9BURK(1-432)> (404 residues with quality score 0.856), released 2010-07-28. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-82.69 7e-030126.082%4NAS-B-XRAY Ribulose-bisphosphate carboxylase [Alicyclobacillus acidocaldarius] <C8WQ56_ALIAD(3-408)> (399 residues with quality score 0.797), released 2013-11-13. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-71.73 1e-03699.082%2OEM-A-XRAY 2,3-diketo-5-methylthiopentyl-1-phosphate enolase [Geobacillus kaustophilus] <MTNW_GEOKA(1-413)> (408 residues with quality score 0.884), released 2007-03-20. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-60.15 3e-03193.081%2OEJ-A-XRAY 2,3-diketo-5-methylthiopentyl-1-phosphate enolase [Geobacillus kaustophilus] <MTNW_GEOKA(1-413)> (407 residues with quality score 0.800), released 2007-03-20. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-58.12 1e-03693.083%2ZVI-A-XRAY 2,3-diketo-5-methylthiopentyl-1-phosphate enolase [Bacillus subtilis] <MTNW_BACSU(1-405)> (395 residues with quality score 0.755), released 2009-09-01. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-48.90 2e-02976.080%3FK4-A-XRAY 2,3-diketo-5-methylthiopentyl-1-phosphate enolase [Bacillus cereus] <MTNW_BACCR(1-414)> (388 residues with quality score 0.802), released 2009-01-13. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
-35.29 7e-01161.072%3QFW-B-XRAY Ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit [Rhodopseudomonas palustris] <Q216E8_RHOPB(2-368)> (352 residues with quality score 0.802), released 2011-02-09. NOTE: This template was deliberately discarded: 5 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).

The 'Total score' in the second column is simply the product of the BLAST alignment score, the WHAT_CHECK [Hooft et al., Nature 381:272] quality score in the PDBFinder2 database [Joosten RP et al., Nucleic Acids Res. 39, D411-D419] and the target coverage. This makes sure that good template structures are used even if the alignment score is lower. The quality score ranges from 0.000 (terrible) to 1.000 (perfect). The target coverage can be artificially low if the alignment scores so badly, that unaligned overhangs on both sides are more favorable.

4. The secondary structure prediction

To aid alignment correction and loop modeling, a secondary structure prediction for the target sequence had to be obtained. This was achieved by running PSI-BLAST to create a target sequence profile and feeding it to the PSI-Pred secondary structure prediction algorithm [Jones DT, J.Mol.Biol. 292:195-202].

The resulting prediction is listed below, the lines 'PreHel', 'PreStr' and 'PreCoi' indicate the estimated probability for the three secondary structure classes helix, strand and coil.

Sequence: MDQSNRYANLNLKEEDLIKNGKHLLVAYKLIPAKGHGFLEVAAHVAAESSTGTNVEVSTTDDFTRGVDALVYEIDETAFGDDPVKGGGLFKVAYPVELFDPNLTDGTYNISHMWSLILGNNQGMGDHQGLRMLDFLVPEMMVRKFDGPSANISNLWKVLGRSETDGGYIAGTIIKPKLGLRPEPFAKACYDFWLGGDFIKNDEPQANQPFCPMEVVMPKVAEAMDRAQQATGQAKLFSANITADYYKEMIHRGDFVLETFAKYNSASHVAFLVDGFVTGPAGVTTARREFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLVRLMGASGMHTGTMGYGKMEGHGKETVLAYMLERDECQGPYFYQKWYGMKATTPIISGGMNALRLPGFFQNLGHGNVINTCGGGAFGHIDSPAAGGISLGQAYDCWKSGSDPIEYAKTHKEFARAFESFPKDGDKLFAGWREKLGVHK
SecStr  : CCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCEEECCCCCCHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCEEEECCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEECCCCCCHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCHHCCCCCCCEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHHHHCCCC
PreHel  : 02443433200000011100000000000000000015788888876543200000000011211000000000000000000000000000001122100011111136667788764212111100000000011488886420000013566777510000000000000121110001447999987654100000000101000001323578899998999987300000000001246888876778899864122221111111111110067776566530000000000122223210000000023221110110000000000000000002688999988876421000000112100000000000000000234444310000000000000000000334445567888999850006888854299999998500679998886676663100
PreStr  : 00000011100100000111027999999855100000000000000000000234321000112111589998755321000001245676533321100000001110000011111111111222478843330000000000001233322111001211002457754421222200000000000001112443100101000000011100000000000000000257765554100000100000000000022111234455422333000000000000025788864232333221000001113455545765433212311100001000000011101110000001332211101112455421013433200000000014566520013310000000012210000000000000000000000000000000000000000000000110
PreCoi  : 97656556688787887778972000000144899884211111123345788765567876666778410001244678999999754333576666799988887653221111225776777787521156666511113468887653211121387888997642244567567797542000012345787656899888899887665421100000000013699742334445553111122221100135766777754423467667832222423458984211135655555567888887764423343234566776677899988897311000000123578998767776798887555578986566555444558864322468986688888665543221110000149992101145700000001499320001113323346799

5. The target sequence profile

To help align target and templates, a target sequence profile has been created from the following multiple sequence alignment, which is built from related UniRef90 sequences (small version, see 'Install' command in the user manual). This alignment has also been saved as Homology_profile.fasta. The color codes are: negative, positive, hydrophilic and hydrophobic.

Target  : MDQSNRYANLNLKEEDLIKNGKHLLVAYKLIPAKGHGFLEVAAHVAAESSTGTNVEVSTTDDFTRGVDALVYEIDETAFGDDPVKGGGLFKVAYPVELFDPNLTDGTYNISHMWSLILGNNQGMGDHQGLRMLDFLVPEMMVRKFDGPSANISNLWKVLGRSETDGGYIAGTIIKPKLGLRPEPFAKACYDFWLGGDFIKNDEPQANQPFCPMEVVMPKVAEAMDRAQQATGQAKLFSANITADYYKEMIHRGDFVLETFAKYNSASHVAFLVDGFVTGPAGVTTARREFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLVRLMGASGMHTGTMGYGKMEGHGKETVLAYMLERDECQGPYFYQKWYGMKATTPIISGGMNALRLPGFFQNLGHGNVINTCGGGAFGHIDSPAAGGISLGQAYDCWKSGSDPIEYAKTHKEFARAFESFPKDGDKLFAGWREKLGVHK
Q0F2Z8  : MDQSNRYADLSLNEADLIAGGKHLLVAYKLIPAKGYGFLEVAAHIAAESSTGTNVEVSTTDDFTRGVDALVYDIDETAFGDEGVTGGGLMKVAYPVELFDPNLIDGHYNVSHMWSLILGNNQGMGDHEGLRMLDFMVPECMIRKFDGPSAGIADLWKVLGRPEVDGGYISGTIIKPKLGLRPEPFAKACLDFWLGGDFIKNDEPQANQPFCPMKVVIPKVAEAMDRAQQETGQAKLFSANATADYHGECVARGEYILSEFAKYGNEKHVAFLIDGFVTGPAGVTTARRAFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLARLQGASGIHTGTMGYGKMEGHGKETVLAYMLERDECMGHYFNQKWYGMKPTAPIISGGMNALRLPGFFENLGHGNVINTCGGGSFGHIDSPAAGGKSLDQAYDCWKSGTDPIEYAKTHGEFARAFESFPGDADKLYPGWRDKLGVHK [uniref90|Q0F2Z8 Ribulose-bisphosphate carboxylase n=1 Tax=Mariprofundus ferrooxydans PV-1 RepID=Q0F2Z8_9PROT]
Q59462  : MDQSNRYADLTLTEEKLVADGNHLLVAYRLKPAAGYGFLEVAAHVAAESSTGTNVEVSTTDDFTRGVDALVYEIDEAAFGDK....GGLMKIAYPVDLFDPNLIDGHYNVSHMWSLILGNNQGMGDHEGLRMLDFLVPEKMVKRFDGPATDISDLWKVLGRPEVDGGYIAGTIIKPKLGLRPEPFAKACYDFWLGGDFIKNDEPQANQNFCPMEVVIPKVAEAMDRAQQATGQAKLFSANVTADFHEEMIKRGEYVLGEFAKYGNEKHVAFLVDGFVTGPAGVTTSRRAFPDTYLHFHRAGHGAVTSYKSPMGMDPLCYMKLARLMGASGIHTGTMGYGKMEGHNDERVLAYMLERDECQGPYFYQKWYGMKPTTPIISGGMDALRLPGFFENLGHGNVINTCGGGSFGHIDSPAAGGISLGQAYACWKTGAEPIE...APREFARAFESFPGDADKIFPGWREKLGVHK [uniref90|Q59462 Ribulose bisphosphate carboxylase n=1 Tax=Hydrogenovibrio marinus RepID=RBL2_HYDMR]
E6QX95  : MDQSARYSDLGLKEEELMKGGKHILVAYTMKPKSGHGYLEAAAHFAAESSTGTNVEVSTTDDFTRGVDALVYHIDEAT..ED.......MRIAYPLELFDRNFTDGRMMIVSFLTLAIGNNQGMGDIEHAKMIDFYVPERAVQLFDGPSRDISDLWRILGRPVVNGGYIAGTIIKPKLGLRPEPFAHAAYQFWLGGDFIKNDEPQGNQVFCPMKKVIPLVADALKRAQDETGQAKLFSANITADDHFEMCGRADFILETFGP..DADKVAFLVDGYVGGPGMVTTARRQYPGQYLHYHRAGHGAVTSPSAKRGYTAFVLAKMSRLQGASGIHVGTMGYGKMEGEHSDKNIAYMIERDEAQGPVYFQKWYGMKPTTPIISGGMNALRLPGFFENLGHGNVINTSGGGAYGHIDSPAAGAISLRQSYECWKAGADPIEFAKEHKEFARAFESFPKDSDLLYPGWREKLGVHK [uniref90|E6QX95 Ribulose bisphosphate carboxylase (RuBisCO) n=1 Tax=mine drainage metagenome RepID=E6QX95_9ZZZZ]
Q31IK3  : MDQSNRYADLSLKEEDLIAGQNHILVAYTMEPAAGYGYLEVAAHIAAESSTGTNVEVCTTDDFTKGVDAIVYDIDEA.........NGIMKVAYPFDLFDRNGLDGKTMIVSFLTLAIGNNQGMGDVKNLQMFDFWVPETKLHLFDGPAVDITNMWKMLGRDKDNGGYIAGTIIKPKLGLRPEPFADAAYQFWLGGDFIKNDEPQGNQTFCPMKKVIPLVADAMKRAQDETGETKLFSANITADDHHEMCYRADYILETFGA..DAPQVAFLVDGYVGGPGMITTARRNYPSQYLHYHRAGHGAITSPSAKRGYTAFVLAKISRLQGASGIHVGTMGYGKMEGDASDKNIAYMIERDECQGPAFYQKWNGMKPTTPIISGGMNALRLPGFFENLGHGNVINTSGGGSYGHIDSPAAGATSLRQSYECWKSGADPIEFAKDHKEFARAFESFPADADKIYPGWREKLGVHK [uniref90|Q31IK3 Ribulose bisphosphate carboxylase n=1 Tax=Thiomicrospira crunogena XCL-2 RepID=RBL2_THICR]
O84917  : .DQSSRYANLDLKESDLIAGGKHILVAYKMKPKAGYDYLATAAHFAAESSTGTNVEVSTTDDFTKGVDALVYFIDEAT..ED.......MRIAYPIELFDRNVIDGRFMIVSFLTLVIGNNQGMGDVEYGKMIDFYVPERAIQMFDGPATDISNLWRILGRPIKDGGYIAGTIIKPKLGLRPEPFAQAAYQFWLGGDFIKNDEPQGNQVFAPVKKVIPLVYDAMKRAQDETGEAKLFSMNITADDYHEMCARADFALEVFGP..DADKLAFLVDGYVGGPGMVTTARRQYPNQYLHYHRAGHGAITSPSSKRGYTAFVLAKMSRLQGASGIHVGTMGYGKMEGEGDDRNIAYMIERDECQGPVYFQKWYGMKPTTPIISGGMNALRLPGFFENLGHGNVINTAGGGSYGHIDSPAAGAKSLRQAYECWKAGADPIEYAKEHKEFARAFESFPGDADKLFPGWRDKLGVHK [uniref90|O84917 Ribulose bisphosphate carboxylase n=4 Tax=Betaproteobacteria RepID=RBL2_THIK1]
C7RNN3  : MDQSNRYADLSLKEEDLIKGGKHILVAYKMKPKAGYDYLPAAAHFAAESSTGTNVEVCTTDDFTRGVDALVYHIDEATEE.........MRIAYPLDLFDRNVTDGRMMIVSFLTLVIGNNQGMGDIEHAKIYDFYMPERAIQLFDGPAKDISDMWRVLGRPVKDGGYIAGTIIKPKLGLRPEPFAKAAYQFWLGGDFIKNDEPQGNQVFAPMKKVMPLVYDAMKRAQDETGQAKLFSANITADDHYEMCARADYILETFGP..DADKVAFLVDGYVGGPGMVTTARRQYPNQYLHYHRAGHGAVTSPSSRRGYDAYVLAKMSRLQGASGIHVGTMGYGKMEGSADDRAIAYVIERDEYQGPAYYQKWYGMKPTTPIISGGMNALRLPGFFANLGHGNVINTSGGGSYGHIDSPAAGAISLRQAYECWKAGADPIAWAREHKEFARAFESFPGDADTLYPGWREKLGVHR [uniref90|C7RNN3 Ribulose-bisphosphate carboxylase n=1 Tax=Candidatus Accumulibacter phosphatis clade IIA str. UW-1 RepID=C7RNN3_ACCPU]
O68486  : LDQTNRYSDLSLKEDELIASGDYVLCAYLMKPKSGYGYLEAAAHFAAESSTGTNVEVSTTDDFTKGVDALVYEIDEAK.........ELMKIAYPVDLFDINIIDGRAMLASFLTLTIGNNQGMGDIEYAKMLDFYMPPKYLRLYDGPAVNIQDMWRILGRPIENGGYIAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEPQGNQPFSPMKKTIPLVADAMRRAQDETGEAKLFSANITADDPAEMIARGEFVLETFGF..EASQVAFLVDGYVAGPTAVATARRNFPNQFLHFHRAGHGAVTSPQSKRGYTAFVHIKMTRLLGASGMHVGTMGYGKMEGEASDKLIAYMIERDSADGPFYHQEWAGMKPTTPIISGGMNALRLPGFFENLGHGNVINTAGGGTYGHIDSPAAGAVSLRQAYECWKEGADPVEYAKEHKEFARAFESFPHDADAIFPGWRDKLGVHK [uniref90|O68486 Ribulose-1,5-bisphosphate carboxylase/oxygenase n=1 Tax=endosymbiont of Riftia pachyptila RepID=O68486_9GAMM]
Q9ZHZ4  : MDQSARYADLSLKEEDLIAGGKHILVAYKMKPKAGHGYLEASAHFAAESSTGTNVEVSTTDDFTKGVDALVYYIDEAT..ED.......MRIAYPMDLFDRNVTDGRMMLVSVLTLIIGNNQGMGDIEHAKIHDIYFPERAIQLFDGPSKDISDMWRILGRPIENGGYIAGTIIKPKLGLRPEPFAAAAYQFWLGGDFIKNDEPQGNQVFCPLKKVLPLVYDSMKRAQDETGQAKLFSMNITADDHYEMMARADFGLETFGP..DADKLAFLVDGFVGGPGMITTARRQYPNQYLHYHRAGHGMITSPSAKRGYTAFVLAKISRLQGASGIHVGTMGYGKMEGEGDDRNIAYMIERDEAQGPVYFQKWYGMKPTTPIISGGMNALRLPGFFENLGHGNVINTAGGGSYGHIDSPAAGAISLKQAYECWKAGADPIEFAKEHKEFARAFESFPKDADAIFPGWREKLGVHK [uniref90|Q9ZHZ4 Ribulose bisphosphate carboxylase n=1 Tax=Halothiobacillus neapolitanus c2 RepID=RBL2_HALNC]
B5EKK0  : MDQSNRYADLSLKEEDLISGGKHILVAYKMKPKAGHGYLEAAAHFAAESSTGTNVEVSTTDDFTKGVDALVYHIDEAT..ED.......MRIAFPLELFDRNVTDGRMMIVSFLTLVIGNNQGMGDIEHGQMIDFFMPPRAIQLFDGPAKDISDLWRILGRPIKDGGYIAGTIIKPKLGLRPEPFAAAAYQFWLGGDFIKNDEPQGNQVFAPVKKTIPLVYDAMKRAMDETGEAKLFSMNITADDHYEMCARADFALETFGP..DADKLAFLVDGFVGGPGMITTARRQYAGQYLHYHRAGHGMITSPSAKRGYTAFVLAKMSRLQGASGIHVGTMGYGKMEGGADDRNIAYMIERDSCDGPVYHQEWYGMKPTTPIISGGMNALRLPGFFENLGHGNVINTAGGGSYGHIDSPAAGAVSLRQAYECWKAGADPIEYAREHKEFARAFESFPGDADKLYPGWREKLGVHR [uniref90|B5EKK0 Ribulose-bisphosphate carboxylase n=4 Tax=root RepID=B5EKK0_ACIF5]
Q8RTI1  : MDQSNRYADLSLKEDDLIKGGNHVLVAYLMKPKTGYGYLEAAAHFSAESSTGTNVEVSTTDDFTKGVDALVYEIDEAK.........EIMKIAYPVDLFDRNITDGRAMIVSFLTLAIGNNQGMGDIAYAKMLDFYVPQKYLRLFDGPSKDISDLWRILGRPVVNGGYIAGTIIKPKLGLRPKPFAEAAYQFWLGGDFIKNDEPQGNQVFSPMRETIPLVYDSMKRAMDETGEAKLFSANITADDHYEMMARGEFILNTFGP..DADKVAFLVDGYVGGPGMVTTARRHFANQYLHYHRAGHGAVTSPSAKRGYTAFVLAKMSRLQGASGIHVGTMGYGKMEGDATDKNIAYMIERDSADGPFYHQEWYGMKPTTPIISGGMNALRLPGFFENLGHANLINTSGGGSYGHIDSPAAGAISLRQAYECWQQGADPIEFAKEHKEFARAFESFPGDADTIFPGWREKLGVHK [uniref90|Q8RTI1 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II n=1 Tax=magnetite-containing magnetic vibrio RepID=Q8RTI1_9PROT]
A1VNQ9  : MDQSNRYADLSLKEEDLIAGGRHILVAYKMKPKAGHGYLEAAAHFAAESSTGTNVEVSTTDEFTKGVDALVYLIDEATEE.........MRIAFPMDLFDRNILDGRMMIVSFLTLVIGNNQGMGDIQHAKIYDFFMPPRAIQLFDGPSKDISDMWRILGRPVKDGGYIAGTIIKPKLGLRPEPFAQAAYQFWLGGDFIKNDEPQGNQTFAPMNKVMPLVHDAMKRAMDETGEAKLFSANITADDHYEMLARGDYILRTFGP..DADKVAFLVDGYVGGPGMITTARRAFPNQYLHYHRAGHGAVTSPSAKRGYDAYVLAKMSRLQGASGIHVGTMGYGKMEGTHDDRAIAYIIERDSYTGPAYHQEWYGMKPTTPIISGGMNALRLPGFFENLGHGNVINTSGGGAYGHIDSPAAGATSLRQAYECWKAKADPIEWAKEHPEFARAFASFPGDADMLFPGWRDKLASHR [uniref90|A1VNQ9 Ribulose bisphosphate carboxylase n=2 Tax=Burkholderiales RepID=RBL2_POLNA]
Q21YM9  : MDQSKRYADLSLQEAALIAGGQHILCAYKMAPKDGLNYLEAAAHFAAESSTGTNVEVCTTDDFTRDVDALVYYVNEAT..ED.......MRIAYPLALFDRNITDGRFMLVSFLTLAVGNNQGMGDIKHAKMIDFYVPERVIQMFDGPAKDISDLWRILGRPVKDGGFIVGTIIKPKLGLRPEPFAQAAYQFWLGGDFIKNDEPQGNQVFSPIKKTLPLVYDALKRAQDETGQAKLFSMNITADDHFEMCARADFALETFGA..DADKLAFLVDGFVGGPGMVTTARRQYPNQYLHYHRGGHGMVTSPSSKRGYTALVLAKMSRLQGASGIHVGTMGHGKMEGAGDDRVMAYMIERDECQGPVYFQKWYGIKPTTPIVSGGMNALRLPGFFDNLGHGNIINTAGGGSYGHLDSPAAGAVSLRQAYECWKAGADPIEWAKEHREFARAFESFPQDADRLFAGWRDKLGV.. [uniref90|Q21YM9 Ribulose bisphosphate carboxylase n=1 Tax=Rhodoferax ferrireducens T118 RepID=RBL2_RHOFD]
C8RX27  : MDQSDRYANLGLKEADLMAGGRHVLVAYIMKPKAGFGFLETAAHFAAESSTGTNVEVSTTDDFTRGVDALVYEINEAT.........GLMKIAYPVELFDHNITDGRAMICSFLTLTIGNNQGMGDVEYAKMHDFWVPPVYLNAFDGPSTTIADLWRVLGRPHVNGGFIVGTIIKPKLGLRPKPFADACYDFWLGGDFIKNDEPQGNQIFAPMRETVKLVSDAMKRAQDKTGMAKLFSFNITADDHYEMVARGEYILEVFGE..NARHVAFLVDGYVTGPAAITTARRRFPDQYLHYHRAGHGAVTSPQSMRGYTAFVLSKMARLQGASGIHTGTMSFGKMEGEASDKLMAFMITDDVAMGPYFKQEWNGMNPTTPIISGGMNALRMPGFFKNLGHSNLILTAGGGAFGHIDGAIAGATSLRQAEQCWKSGADPIEFAKSHREFARAFESFPGDADKLYPGWRKALGV.. [uniref90|C8RX27 Ribulose-bisphosphate carboxylase n=1 Tax=Rhodobacter sp. SW2 RepID=C8RX27_9RHOB]
A1AWY1  : MDQSNRYADLLLDEETLIKEGNHFLVAYTMTPMPGFGYLETAAHFAAESSTGTNVEVSTTDDFTKDLDAMVYEIDEAK.........GTMKIAYPNNLFDRNLIDGRAMVVSLLTLIIGNNQGMGDVQCAQIQDFWISRKFLEIFDGPSLDITDLWSILGRSRTDGGYIAGTIIKPKLGLRPKPFSEAAYQFWLGGDFIKNDEPQGNQVYARMKDVTPLVADAMRRAQDETSEAKIFSANITADDHHEMCARADYILETFAE..NAHHVAFLVDGYVGGCGMITTARRNYPNQYLHYHRAGHGAITSPSSVRGYTAFVLGKLSRLMGASGIHVGTMGYGKMEGGADDRNIAYMIERDSADGPVYHQEWFGMKPTTPIISGGMNALRLPGFFENLGHGNVINTSGGGSYGHIDSPAAGAKSLRQAYDCWMAKADPIEFAKDHNEFARAFESFPNDADSLYPGWRDKLGIHK [uniref90|A1AWY1 Ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit n=5 Tax=Bacteria RepID=A1AWY1_RUTMC]
Q479W5  : MDQSNRYADLSLTEAELIAGGQHILCAYKMKPKAGHRYLEAAAHFAAESSTGTNVEVCTTDEFTKGVDALVYHIDEAS..ED.......MRIAYPLDLFDRNMTDGRMMMASFLTLTIGNNQGMGDIEHAKMVDFYVPRRGIELFDGPSKDISDLWRMLGRPVKDGGYIAGTIIKPKLGLRPEPFARAAYEFWLGGDFIKNDEPQGNQVFAPLKKVIPLVYDSMKRAMDETGEAKLFSMNITADDHFEMCARADFALEAFGP..DADKLAFLVDGYVGGPGMITTARRQYPNQYLHYHRAGHGAVTSPSSKRGYTAYVLAKMSRLQGASGIHVGTMGYGKMEGDKDDRACAYIIERDSYTGPVYHQEWYGMKPTTPIISGGMNALRLPGFFENLGHGNVINTAGGGAYGHIDSPAAGARSLRQAYDCWKAGADPVEWARDHYEFARAFESFPQDADQLYPGWRHKL.... [uniref90|Q479W5 Ribulose bisphosphate carboxylase n=1 Tax=Dechloromonas aromatica RCB RepID=RBL2_DECAR]
Q2J1J9  : MDQSSRYANLNLKESDLIAGGRHVLCAYIMKPKDGFGFLQTAAHFSAESSTGTNVEVSTTDDFTRGVDALVYEIDEA.........NNVMKIAYPIELFDRNVIDGRAMIASFLTLTIGNNQGMGDVEYAKMHDFYVPPAYLRLFDGPSTTIRDLWRVLGRPVVDGGFIVGTIIKPKLGLRPQPFADACYDFWLGGDFIKNDEPQGNQVFAPFKETVRAVNEAMRRAQDKTGEPKLFSFNITADDHYEMVARGEYILETFA..DNADHVAFLVDGYVAGPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHTGTMGFGKMEGEAADRAMAYMITEDSADGPFFHQEWLGMNPTTPIISGGMNALRMPGFFDNLGHSNLIMTAGGGAFGHIDGGAAGAKSLRQAEQCWKAGADPVEFAKDHREFARAFESFPHDADALYPNWRNSL.... [uniref90|Q2J1J9 Ribulose bisphosphate carboxylase n=8 Tax=Rhodopseudomonas palustris RepID=RBL2_RHOP2]
Q2RRP5  : MDQSSRYVNLALKEEDLIAGGEHVLCAYIMKPKAGYGYVATAAHFAAESSTGTNVEVCTTDDFTRGVDALVYEVDEAR.........ELTKIAYPVALFDRNITDGKAMIASFLTLTMGNNQGMGDVEYAKMHDFYVPEAYRALFDGPSVNISALWKVLGRPEVDGGLVVGTIIKPKLGLRPKPFAEACHAFWLGGDFIKNDEPQGNQPFAPLRDTIALVADAMRRAQDETGEAKLFSANITADDPFEIIARGEYVLETFGE..NASHVALLVDGYVAGAAAITTARRRFPDNFLHYHRAGHGAVTSPQSKRGYTAFVHCKMARLQGASGIHTGTMGFGKMEGESSDRAIAYMLTQDEAQGPFYRQSWGGMKACTPIISGGMNALRMPGFFENLGNANVILTAGGGAFGHIDGPVAGARSLRQAWQAWRDGVPVLDYAREHKELARAFESFPGDADQIYPGWRKALGV.. [uniref90|Q2RRP5 Ribulose bisphosphate carboxylase n=2 Tax=Rhodospirillum rubrum RepID=RBL2_RHORT]
Q2W3S5  : MDQSKRYVNLGLREADLIKGGRHVLCAYRMRPRPGHGYVETAAHFAAESSTGTNVEVCTTDDFTRGVDALVYEVDEAE.........GLMKIAYPVELFDRNIIDGKAMIASFLTLTVGNNQGMSDVENAKMEDFYVPPDFLTLFDGPARNIAHMWKVLGRPEVNGGMVVGTIIKPKLGLRPKPFADACHQFWLGGDFIKNDEPQGNQVFAPFKDTMRLVADSMRRAQDETGQAKLFSANITADDPAEMIARGQFILDTFGE..NASHVAFLVDGFVAGPTAVTTCRRNFPDTFLHYHRAGHGAITSRQSKRGYSVLVHMKMARLLGASGIHTGTMGYGKMEGAPDEKVVAYMLERPTAEGPHYRQDWGDMRACTPIISGGMNALRLPGFFDNLGHSNVIQTSGGGAFGHKDGPVAGALSLRQAHEAWMRGISLVEYAQGHPELRGAFESFASDADRLYPGWRDRLRI.. [uniref90|Q2W3S5 Ribulose bisphosphate carboxylase n=2 Tax=Magnetospirillum RepID=RBL2_MAGSA]
A3PRW6  : MDQSNRYARLDLKEADLIAGGRHVLCAYVMKPKAGYGYLETAAHFAAESSTGTNVEVSTTDDFTRGVDALVYEID.......PEKE..IMKIAYPVELFDRNIIDGRAMLCSFLTLTIGNNQGMGDVEYAKMHDFYVPPCYLRLFDGPSMNIADMWRVLGRDVRNGGMVVGTIIKPKLGLRPKPFADACHEFWLGGDFIKNDEPQGNQTFAPLKETIRLVADAMKRAQDETGEAKLFSANITADDHYEMVARGEYILETFGE..NADHVAFLVDGYVTGPAAITTARRQFPRQFLHYHRAGHGAVTSPQSMRGYTAFVLSKMARLQGASGIHTGTMGYGKMEGEAADKIMAYMLTDEAAEGPFYRQDWLGLKATTPIISGGMNALRLPGFFDNLGHSNVIQTSGGGAFGHLDGGTAGAKSLRQSHEAWMAGVDLVTYAREHRELARAFESFPADADKFYPGWRDRL.... [uniref90|A3PRW6 Ribulose bisphosphate carboxylase n=8 Tax=Rhodobacter RepID=RBL2_RHOS1]
E6VVI6  : .DQTSRYVNFDLKEDQLIADGNHVLCAYIYKPANGYGNVEVAAHFAAESSTGTNVEVCTTDDFTKGVDALVYEVSDASNGDS......LMKIAYPVELFDRNIIDGRAMLASFLTLCIGNNQGMGDVAYAKMHDFYVPRQYLELFDGPSKNIADFWRMLGRPTENGGMIAGTIVKPKLGLRPKPFADACYHFWLGGDFVKNDEPQGNQVFAPLKETITAVADAMRRAQDETGEAKIFSANITADDPREMIARGEFILNAFGE..NASRVAFLVDGYVAGPTAITTARRNFPNQFLHYHRAGHGAVTSPQAKRGYTAFVLSKMSRLQGASGIHTGTMGFGKMEGEMADKSMAYMIEREEAQGPYFKQKWYGMKATTPMISGGMNALRLPGFFDNLGHSNICQTSGGGAFGHLDGPTAGALSLRQSHDAWIQGVNLLDYAKEHNELARAFESFPGDADRFYPTWRHQL.... [uniref90|E6VVI6 Ribulose-bisphosphate carboxylase n=1 Tax=Desulfovibrio aespoeensis Aspo-2 RepID=E6VVI6_DESAO]
A4U3D1  : MDQSKRYCNLALNEAELMAQGRHVLCAYIFKPKAGYEPIATAAHFAAESSTGTNVEVCTTDDFTRGVDALVYEVTEQANGDH......LMKIAYPNDLFDRNLIDGRAMIVSFLTLTIGNNQGMSDVEYAKMHDFWMPPAMLQLFDGPAMNIADMWRVLGRPQVNGGMVVGTIIKPKLGLRPKPFADACHQFWLGGDFIKNDEPQGNQVFAPMREVIPLVADALRRAQDETGEAKLFSANITADDPFEMIKRGEMILETFGE..NANRVAFLVDGYVGGPSAITLARRYFPNQFLHYHRAGHGAVTSKQSKRGYSVLTHMKMARLQGASGIHTGTMGYGKMEGDKDEKMVAYMLERDVADGLYFRQDWQGIKATTPIISGGMNALRLPGFFDNLGHSNVIQTSGGGAFGHKAGGTVGAKSLRLAHEAWVRGINLVDFAQEHPELKGAFESFPQDADALYPGWRDKLKV.. [uniref90|A4U3D1 Ribulose bisphosphate carboxylase, large chain n=1 Tax=Magnetospirillum gryphiswaldense RepID=A4U3D1_9PROT]
E3T308  : MDQSARYADLSLKEDDLIKGGKHVLCAYTMQPAAGYGYLEVAAHIAAESSTGTNVEICTTDDFTKGVDALVYYCNEAE.........GVIKIAYPMDLFDRNLTDGRTMIVSFLTLCIGNNQGMGDCKNLQMQDFYMPERMLQLFDGPQKDISDMWRILGRPVKDGGYIAGTIIKPKLGLRPEPFAKAAYQFWLGGDFIKNDEPQGNQVFCPMKKVMPLVVDAMRRAEDETGQAKLFSANITADCHDEMIARGEYILETFGP..DADKCALLVDGYVGGPGMVTTARRHFADQYLHYHRAGHGAVTSPSSVRGYTALVLSKMSRLQGASGIHVGTMGFGKMEGGADDRIIAYMIEQDSADGTYYHQEWYGMKPTTPIISGGMNALRLPGFFENLGHGNVINTSGGGSYGHIDSPAAGATSL................................................. [uniref90|E3T308 Ribulose-bisphosphate carboxylase (Fragment) n=1 Tax=uncultured organism RepID=E3T308_9ZZZZ]
E3T318  : LDQTSRYSDLNLKEEELIASGNYVLTAYKMRPKPGFDFIGTAAHFCAESSTGTNVQVVTTDDFTKNLDSICYFVDEEK.........ELMKIAYPIDLFDRNITDGRAMVVSMMTLIVGNNQGMGDVEYAKLLDFYVPPKFLRLFDGPSMNIQDMWRILERDLENGGMVVGTIIKPKLGLRSKPFADACYQFWLGGDFIKNDEPQGNQLYAPMREITPLVADAMKRAMDDTGQAKIFSANITADDPFEMIARGEYILETFGEH..AENVAFLVDGYVGGCGMVTLARRYFPNQFLHYHRAGHGAITSEESNRGYTALAHMKWARMSGASGIHVGTMGYGKMEGYASDKVNALMLVDDDVEGDHFHQNWGKMKSCTPIISGGMNALRLPGFFDNLGHCNVIQTSGGGALGHKDGIVAGATSLRQAFTAWQEGVDLVDYAKEHEELRGALETFQEDADNLYPGWREKLGVHK [uniref90|E3T318 Ribulose bisphosphate carboxylase n=1 Tax=uncultured organism RepID=E3T318_9ZZZZ]
E3T313  : MDQSSRYVNLNLNEKELINAGNHVLVYYKMLPSSQNDYLAAAAHFAAESSTGTNVEVSTTDEFTKSVDAIVYDVK.......PAEEE..MRIAYPLELFDRNIIDGRAMIVSFLTLCIGNNQGMGDIVHAKMYDFYVPPKFLALFDGPSKGIEDMWRTLGRPVKNGGFIVGTIIKPKLGLQPKPFADAAYDFWLGGDFIKNDEPQGNQVFAPMKKTIPLVVDALKKAQDKTGKAKLFSANITADDPFEIIARGEYILEQFGEY..ASHVAFLIDGYVGGPTAITTARRYFPNQFIHYHRAGHGAVTSPSSKRGYSAFVLSKMARLQGASGIHVGTMSFGKMEGEKDDKRIAFMIENEKAEGIVYAQEWLGMKPTTPIISGGMNALRVGGFFENMGHSNVIMTAGGGCYGHIDGASEGAESMRQAEQCWKEGADVFEFAKEHRQFARAFVSFPHDADKFYPGWRDKL.... [uniref90|E3T313 Ribulose bisphosphate carboxylase n=1 Tax=uncultured organism RepID=E3T313_9ZZZZ]
D9J1X1  : LDQSNRYAKLDLDEETLIKEQQHVLVAYKMRPKYAVDYVSTAAHFAAESSTGTNVNVCTTDDHTMSVDAVVYEVDE....DEE.....LMKIAYPVKLFDRNITDGRAMVCSILTLVIGNNQGMGDVEYGKIHDIFIPPNFLRLFDGPAVDIRHMWRVLGRTEWNGGFVVGTIIKPKLGLRPKEFAEAAYQFRLGGDFLKNDEPQGNQTFCPMRTVIPIVVEAMKRAMAETGRRVFFSANITADDPDEMIARGKYVLGQFD..HLAEQVSLLVDGYVAGPTAVTTSRRNFPRQYLHYHRAGHGAVTSPQTQRGYTALVLSKISRMLGASGIHVGTMGYGKMESEKSDKDIVYMLERDIAQGPYYKQDWAGMLPTTGIISGGMNAVRMVGFFENLTHANVIMTCGGGSYGHVDGPAEGATSCRQAWLCWKAGEDPIEYAKKHRQYARAFISFPGDADKLFPNWRTELGLH. [uniref90|D9J1X1 Plastid ribulose-1,5-bisphosphate carboxylase oxygenase n=1 Tax=Chromera velia RepID=D9J1X1_9ALVE]
Q41406  : LDQSSRYADLSLDEDTLIRNGKHVLVAYIMKPKAGYDYLATAAHFAAESSTGTNVNVCTTDDFTKSVDALVYYIDP....DNEE.....MKIAYPTLLFDRNITDGRGMMCSFLTLAIGNNQGMGDVEYGKIYDFYLPPAFLRLYDGPSVNVEDMWRILGRGTTNGGLVVGTIIKPKLGLQPKPFGEACYSFWQGGDFIKNDEPQGNQVFCQMNECIPEVVKAMRACVKETGSSKLFSANITADDPEEMIARGKYIMSQFGPLSE..NCAFLVDGYVAGGTAVTCCRRNFPKQFLHYHRAGHGSVTSPQTQRGYTAFVHTKISRVIGASGIHVGTMSFGKMEGDASDKNIAYMLQDDEADGPYYRQEWQGMKETTPIISGGMNALRLPAFFENLGHSNVILTAGGGSFGHKDGPKIGAISCRQGEEAWKSLSDVIEYAKTHEEIKGAFLTFQKDADQIYPGWKEKLG... [uniref90|Q41406 Ribulose bisphosphate carboxylase (Fragment) n=54 Tax=root RepID=RBL2_SYMSP]
Q6Y9H0  : LDQSSRYADLSLTEEDLIKNGQHVLVAYIMKPKAGYDYLATAAHFAAESSTGTNVNVCTTDDFTKTVDALVYYIDPE.........NEEMKIAYPTALFDRNITDGRAMMCSVLTLSIGNNQGMGDVDYGKIYDIYFPPQYLRLFDGPSCCVIDMWRILGRGTVGGGLVVGTIIKPKLGLQPKPFGQACYGFWQGGDFIKNDEPQGNQTFCQMNECIPEVVKAMRAAQEETGQGKLFSANITADDPNEMIARAKYILNQMGPM..AENCAFLVDGYVAGGTAVTVARRNFPKQFLHYHRAGHGAVTSPQTQRGYTAFVHTKLSRVIGASGIHTGTMSFGKMEGDASDKNIGFMLQDDVADGPYYRQEWEGMKQTTPIISGGMNALRLPAFFENLGHSNVILTAGGGAFGHKDGPKQGAISCAQGEESWKSLSDVVEYAKTHEELKGAFLTFQKDADQIYPGWKEKLG... [uniref90|Q6Y9H0 Ribulose bisphosphate carboxylase (Fragment) n=62 Tax=root RepID=RBL2_PROMN]
Q5ENN5  : LDQSSRYADLSLSEEQLIANGKHVLVSYIMKPKAGYDYLATAAHFAAESSTGTNVNVCTTDDFTKSVDALVYYIDPE.........NEECKIAYPNLLFDRNIIDGRAMMCSVLTLTIGNNQGMGDVEYGKIYDIYFPPSYLRLFDGPSCNIIDMWRILGRGTTDGGLVVGTIIKPKLGLQPKPFGEACYAFWQGGDFIKNDEPQGNQPFCQMNEVIPEVVKAMRAAIKETGVAKLFSANITADDPAEMIARGKYVLAQFGPLSE..NCAFLVDGYVAGGTAVTVARRNFPKQFLHYHRAGHGSVTSPQTQRGYTAFVHTKLSRVQGASGIHVGTMSFGKMEGDASDKNIAFMLQDDAADGPYYHQTWEGMAETTPIISGGMNALRLPAFFENLGHSNVILTAGGGAFGHKDGPKQGATSCRQAWKLWKAGSDVIEYAKTHEEIKGAFLTFQKDADQIYPGWKEKLG... [uniref90|Q5ENN5 Ribulose bisphosphate carboxylase, chloroplastic n=1 Tax=Heterocapsa triquetra RepID=RBL2_HETTR]
Q9FPW1  : LDQSSRYADLSLDEATLVKNGKHVLVAYIMKPKAGYDYLATAAHFAAESSTGTNVNVCTTDDFTKSVDALVYYIDPDSEE.........MKIAYPTLLFDRNIIDGRGMMCSFLTLAIGNNQGMGDVEYGKIYDFYLPPSFLRLYDGPAVNVEDMWRILGKGTSNGGLVDGTIIKPKLGLQPNPFGEACYSFWQGGDFIKNDEPQGNQVFCQMNECIPEVVKAMRACVKETGSSKLFSANITADDPEEMIARGKYIMSQFGPLSE..NCAFLVDGYVAGGTAVTCCRRNFPKQFLHYHRAGHGSVTSPQTQRGYTAFVHTKISRVIGASGIHVGTMSFGKMEGDASDKNIAYMLQDDEADGPYYRQEWQGMKETTPIISGGMNALRLPAFFENLGHSNVILTAGGGSFGHKDGPKIGAISCRQGEEAWKSLSDVIEYAKTHEEIKGAFLTFQKDADQIYPGWKEKLG... [uniref90|Q9FPW1 Ribulose 1,5-bisphosphate carboxylase oxygenase large subunit n=1 Tax=Symbiodinium sp. RepID=Q9FPW1_SYMSP]
Q42813  : LDQSSRYADLSLTEEDLVKNGKHVLVAY.IMNQGGYDYLATAAHVAAESSTGTNVNVCTTDDFTKTVDALVYYIDPE.........NEEMKIAYPVPLFDRNITDGRAMMCSVLTLSIGNNQGMGDVEYGKIYDIYFPPSYLRFFDGPACSILDMWRILGRDMTDGGLVVGTIIKPKLGLQPKPFGEACYAFGQGGDFIKNDEPQGNQVFCQMNECIPEVVTAMKACIKETGSEKLFSANITADDPAEMIARGKYILGQFGPM..AENCAFLVDGYVAGGTAVTVARRNFPKQFFHYHRAGHGAVTSPQTQRGYTAFVHTKISRVIGASGIHVGTMSFGKMVGDASDKGIAYMLQQDAAGGPYYHQKWEGVVQTTPIISGGMNALRLPAFFENLGHSNVILTAGGGTFGHKDGPKQGATSCRQAWKLWKAGTGVIEYAKTHEEIKGAFLTFQKDSDQIYPGWKEKLG... [uniref90|Q42813 Ribulose 1,5-bisphosphate carboxylase, chloroplastic (Fragment) n=1 Tax=Gonyaulax polyedra RepID=RBL2_GONPO]
Q2MYY5  : ......................................................................................................................GNNQGMGDHEGLRMLDFLVPESMVKRFDGPATDISDLWKILGRPEVDGGYIAGTIIKPKLGLRPEPFAKACYDFWLGGDFIKNDEPQANQPFCPMEVVIPKVAEAMDRAQQATGQAKLFSANVTADFHEEMIKRGEYVLSEFAKYGNEKHVAFLVDGFVTGPAGVTTSRRAFPDTYLHFHRAGHGALTSYKSPMGMDPLCYMKLARLMGASGIHTGTMGYGKMEGHNDERVLAYMLERDECQGPYFYQKWYGMKPTTPIISGGM........................................................................................ [uniref90|Q2MYY5 Form II ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (Fragment) n=1 Tax=Thiomicrospira kuenenii RepID=Q2MYY5_9GAMM]
Q5DVV2  : ............................................................................................................................................................................IIKPKLGLRPAPFAKACYDFWLGGTFIKNDEPQANQPFCPMEEVIPLVAESMDRAQQETGEAKLFSANITADFHEEMIKRGEFVLDAFAKYNSADHVAFLVDGFVTGPAGVTTCRRAFPDTFLHFHRAGHGALTSYKSPMGMDPLCYMKLARMMGASGIHTGTMGYGKMEGHAGETVLAYMLERDECQGPYFYQKWYGMKATTPIICGGMNA...................................................................................... [uniref90|Q5DVV2 Ribulose-1,5-bisphosphate carboxylase oxygenase large subunit (Fragment) n=1 Tax=uncultured prokaryote RepID=Q5DVV2_9ZZZZ]
Q5DVV0  : ............................................................................................................................................................................IIKPKLGLRPEPSAKACYEFWLGGDFIKNDEPQANQPFCPMEEVIPLVAEAMDRAQQETGEAKLFSANITADFYKEMIRRGEYILEQLAKYGNEKHVAFLVDGFVTGPAGVTTARREFPDVFLHFHRAGHGAITSYKSPMGMDPICYMKLARLMGASGIHTGTMGYGKMEGHKDERVLPYMLERDECQGPYFYQKWYGMKPATPIISGGMNA...................................................................................... [uniref90|Q5DVV0 Ribulose-1,5-bisphosphate carboxylase oxygenase large subunit (Fragment) n=1 Tax=uncultured prokaryote RepID=Q5DVV0_9ZZZZ]
F2ZCF5  : ......................................................................................................................GNNQGMGDVACAQMFDFYVPPYMLNLFDGPAVDISDLWRLLGRDHKNGGYIAGTIIKPKLGLRPKPFAEAAYQFWLGGDFIKNDEPQGNQVFSPVKETIPLVADAMKRAQDETGEAKIFSMNITADDYHEMCARADFALEVFGE..DAPRLAFLVDGYVGGPGMVTTARRQYPDQYLHYHRAGHGAVTSPSSKRGYTAYILAKMARLIGASGIHVGTMGYGKMEGSTDDTIIAYMVERDECQGPVYYQKWYGMKPTTPIISGGMNALR.................................................................................... [uniref90|F2ZCF5 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=2 Tax=uncultured bacterium RepID=F2ZCF5_9BACT]
F2ZCE0  : ......................................................................................................................GNNQGMGDVANLQMFDFWVPETKLHLYDGPSVDISHMWKLLGRPRVNGGYIAGTIIKPKLGLRPEPFADAAYQFWLGGDFIKNDEPQGNQVFCPMKKVIPMVVDSMKRAQDETGEAKLFSANITADDYHEMCYRADFVLESFGEF..APHVAFLVDGYVGGPGMVTTARRNYPSQYLHYHRAGHGAVTSPSSKRGYTAFVLAKLSRLMGASGIHVGTMGYGKMEGGNDDRIIAYMIERDECQGPVYYQKWEGMKPTTPIIS........................................................................................... [uniref90|F2ZCE0 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=2 Tax=uncultured bacterium RepID=F2ZCE0_9BACT]
F5BZE4  : ......................................................................................................................GNNQGMGDVDYAKMHDFYVPREMVTLFDGPAMNITDMWRVLGRPQVNGGMVVGTIIKPKLGLRPKPFADACHQFWLGGDFIKNDEPQGNQVFAPLKDTMILVADAMERAQQETGEAKIFSANITADDPFEMIRRGELILEIFGK..NASHVAFLVDGYVAGPTAITTCRRYFPGQFLHYHRAGHGAVTSKQSKRGYNVLTHMKMARLQGASGIHTGTMGYGKMEGDKNEKMVAYMLERDEADGVYYRQDWHGMKATTPIISGGMNALR.................................................................................... [uniref90|F5BZE4 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II (Fragment) n=3 Tax=unclassified Alphaproteobacteria (miscellaneous) RepID=F5BZE4_9PROT]
E9NHE6  : ......................................................................................................................GNNQGMGDIEHAKMIDFYMPERAIQLFDGPARDISDMWRILGRPIKDGGYIAGTIIKPKLGLRPEPFAHAAYQFWLGGDFIKNDEPQGNQVFCPTKKVIPLIVDALRRAQDETGQAKLFSANITADDHYEMCARADYILEAFGP..DADKVAFLVDGYVGGPGMVTTARRQYPGQYLHYHRAGHGAVTSPSAKRGYTAFVLAKMSRLQGASGIHVGTMGYGKMEGDADDKIIAYMIERDECQGPVYFQKWYGMKPTTPIISGGMNALR.................................................................................... [uniref90|E9NHE6 Ribulose 1,5-bisphosphate carboxylase/oxygenase (Fragment) n=3 Tax=Bacteria RepID=E9NHE6_9GAMM]
Q2MYY7  : ......................................................................................................................GNNQGMGDVKNLQMFDFWVPETKLHLFDGPAVDITNMWKMLGRDKDNGGYIAGTIIKPKLGLRPEPFADAAYQFWLGGDFIKNDEPQGNQTFCPMKKVIPLVADAMKRAQDETGETKLFSANITADDHHEMCYRADYILETFGA..DAPQVAFLVDGYVGGPGMITTARRNYPSQYLHYHRAGHGAITSPSAKRGYTAFVLAKISRLQGASGIHVGTMGYGKMEGDASDKNIAYMIERDECQGPAFYQKWNGMKPTTPIISGGM........................................................................................ [uniref90|Q2MYY7 Form II ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (Fragment) n=1 Tax=Thiomicrospira crunogena RepID=Q2MYY7_9GAMM]
F5BZE6  : ......................................................................................................................GNNQGMGDVEYAKMIDFYMARSLLTLFDGPAMNITDMWRVLGRPQVNGGMVVGTIIKPKLGLRPKPFADACYMFWMGGDFIKNDEPQGNQVFAPTREIIPLVAEAMERAQQETGEAKIFSANITADDPFEMIRRGEFILEAFGK..NASHVAFLVDGYVGGPSAVTLCRRYFPNQFLHYHRAGHGAVTSNQSKRGYTVLTHMKMSRLQGASGIHTGTMGYGKMEGDKNEKMVAYMIERDEAMGVYYNQPWHGMTATTPIISGGMNALR.................................................................................... [uniref90|F5BZE6 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II (Fragment) n=1 Tax=alpha proteobacterium LM-5 RepID=F5BZE6_9PROT]
Q2MYY6  : ......................................................................................................................GNNQGMGDVKNLQMVDFWVPETKLHLFDGPAKDISDMWRVLGRDYKNGGYIAGTIIKPKLGLRPEPFAAAAYQFWLGGDFIKNDEPQGNQVFAPMKKVMPLVVDAMKRAQDETGQAKLFSANITADDHYEMLYRADYILEAFGEF..AQNVAFLVDGYVGGPGMITTARRNYPSQYLHYHRAGHGAITSPSANRGYTAFVLSKISRLQGASGIHVGTMGFGKMEGGNEDKNIAYMIERDECQGPFFYQKWNGMKPTTPIISGGM........................................................................................ [uniref90|Q2MYY6 Form II ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (Fragment) n=1 Tax=Thiomicrospira pelophila RepID=Q2MYY6_9GAMM]
Q27PR8  : ......................................................................................................................GNNQGMGDVKNLQMYDFWVPESKLYLFDGPATDISDMWRMLGRPVENGGYVAGTIIKPKLGLRPEPFADAAYQFWLGGDFIKNDEPQGNQTFCPMKKVIPLVADAMKRAQDETGEAKLFSANITADDHHEMCYRADYILETFGE..DAPKVAFLVDGYVGGPGMVTTARRNYASQYLHYHRAGHGAVTSPSSKRGYTAFVLAKMSRLQGASGIHVGTMGYGKMEGDASDKIIAYMIERDECQGPAFYQKWNGMKPTTPIISGGM........................................................................................ [uniref90|Q27PR8 Form II ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit (Fragment) n=2 Tax=Bacteria RepID=Q27PR8_9GAMM]
F2ZCD3  : ......................................................................................................................GNNQGMGDVEYAKMYDFYMPPEMLKIFDGPSTTISDLWRVLGRPHVDGGFIVGTIVKPKLGLRPEPFARACYDFWLGGDFIKNDEPQGNQVFAPLKETIPLVADAMKRAQDDTGEAKLFSANITADDHYEMVARGEFILETFAE..NADHVAFLVDGYVTGPAAITTARRQFPNQYLHYHRAGHGAVTSPQAKRGYTAFVLSKMARLQGASGIHTGTMSYGKMEGEKSDTDMAYMIMQDSADGPFYHQEWLGMNPTTPIISGG......................................................................................... [uniref90|F2ZCD3 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=3 Tax=uncultured bacterium RepID=F2ZCD3_9BACT]
Q0PQW3  : .....................................................................................................................................................................................................FIKNDEPQGNQPFSPMRKTIPLVADAMRRAQDETGEAKLFSANITADDPAEMIARGEFVLETFGF..EASQVAFLVDGYVAGPTAVATARRNFPNQFLHFHRAGHGAVTSPQSKRGYTAFVHIKMTRLLGASGMHVGTMGYGKMEGEASDKLIAYMIERDSADGPFYHQEWAGMKPTTPIISGGMNALRLPGFFENLGHGNVINTAGGGAYGHIDSPAAGAVSLRQAYECWKEGADPVEYAKEHKE........................... [uniref90|Q0PQW3 Ribulose-15-bisphosphate carboxylase/oxygenase form II large subunit (Fragment) n=1 Tax=Endoriftia persephone 'Hot96_1+Hot96_2' RepID=Q0PQW3_9GAMM]
F5BZE5  : ......................................................................................................................GNNQGMGDIEYAKMQDFYVPPAYLQLFDGPSVNITEMWRVLGRPQSNGGMVVGTIIKPKLGLRPEPFAKACYDFWLGGDFIKNDEPQGNQVFAPLKETIRLVADSMKRAQDKTGQPKLFSANVTADDPAEMLARGHYILETFGP..NASHVAFLVDGFVGGPTSVTLARRNFPSQFLHYHRAGHGMVTSNQSKRGYNVLVHMKMARLQGASGIHTGTMGYGKMEGDPSDKIVAYMLEKDVADGLYYRQDWQGMKACTPIISGGMNALR.................................................................................... [uniref90|F5BZE5 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II (Fragment) n=1 Tax=alpha proteobacterium LM-1 RepID=F5BZE5_9PROT]
F2ZCD1  : ..................................................................................................................................KIYDFFVPPKFLQQFDGPSMDISDMWRTLGRPLVNGGYIAGTIIKPKLGLRPKPFAEAAYQFWLGGDFIKNDEPQGNQTFCPLKKVLPLVADAMKRAQDETGEAKLFSANITADDHYEMLARADYVLETFAE..NASHVAFLVDGFVGGPGMITTARRNYPNQYLHYHRAGHGMVTSPSAKRGYDAFVLAKLSRLQGASGIHVGTMGFGKMESGNDDKIIAYMIERDECQGPVYYQKWFGMKPTTPIISGGMNALR.................................................................................... [uniref90|F2ZCD1 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=1 Tax=uncultured bacterium RepID=F2ZCD1_9BACT]
F5BZE7  : ......................................................................................................................GNNQGMGDVEYAKMHDFWVPPAMLQLFDGPAMNIADMWRVLGRPQVNGGMVVGTIIKPKLGLRPKPFADACHQFWLGGDFIKNDEPQGNQVFAPMREVIPLVADALRRAQDETGEAKLFSANITADDPFEMIKRGEMILETFGE..DANRVAFLVDGYVGGPSAITLARRYFPGQFLHYHRAGHGAVTSKQSKRGYSVLTHMKMSRLQGASGIHTGTMGYGKMEGEKDEKMVAYMLERDVADGIYYRQDWQGMKATTPIISGGMNALR.................................................................................... [uniref90|F5BZE7 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II (Fragment) n=4 Tax=Alphaproteobacteria RepID=F5BZE7_9PROT]
F5BZE1  : ........................................................................................................................NQGMGDVEYAKMLDFYVPPAYLRLFDGPACNIRDMWRVLGRPQENGGMVVGTIIKPKLGLRPKPFADACHQFWLGGDFIKNDEPQGNQVFAPLKETIRLVADAMDRAQDATGQPKLFSANITADDPAEMLARGHYILETFGK..NASHVAFLVDGYVGGPTAITLCRRNFPNQFLHYHRAGHGAVTSSQSKRGYTVLVHMKMARLQGASGIHTGTMGYGKMEGEPGEKMVAYMLENDVAEGSHFRQEWLGMKACTPIISGGMNALR.................................................................................... [uniref90|F5BZE1 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II (Fragment) n=1 Tax=alpha proteobacterium SS-4 RepID=F5BZE1_9PROT]
F2ZCF4  : ......................................................................................................................GNNQGMGDVKDAQMFDFHVPKQMLDIFDGPSMDITDLWNLLGRSRTDGGYIAGTIIKPKLGLRPKPFADAAYQFWLGGDFIKNDEPQGNQKYARMKTVTPLVADAMKRAQDETGEAKIFSANITADDHHEMIARGEYILEAFGE..NANHVAFLVDGYVGGCGMVTTARRNFADQYLHYHRAGHGCITSPSSVRGYTAFVLAKLSRLMGASGIHVGTMGFGKMEGGADDRHIAYMIEQDSAQGPVYHQEWFGMKPTTPIISGGMNALR.................................................................................... [uniref90|F2ZCF4 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=3 Tax=uncultured bacterium RepID=F2ZCF4_9BACT]
F2ZCD0  : ......................................................................................................................GNNQGMGDIANAQMQDFYVPPAMLALFDGPAKSINDLWTLLGRDNENGGYIAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEPQGNQVFCPLKKVLPLVHDAMKRAQDETGEAKLFSLNITADDHYEMCARADFGLETFGE..DAPRLAFLVDGFVGGPGMVTTARRQYSSQYLHYHRAGHGMITSPSSKRGYTAYILAKMSRLMGASGIHVGTMGYGKMEGGADDKIIAYMIERDECQGPFYYQKWHGMKPTTPIVSGGM........................................................................................ [uniref90|F2ZCD0 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=4 Tax=uncultured bacterium RepID=F2ZCD0_9BACT]
F5BZE3  : ......................................................................................................................GNNQGMGDVEHAKMEDFWVPPDFLTLFDGPAVNISHMWKVLGRPEDNGGMVVGTIIKPKLGLRPKPFADACHQFWLGGDFIKNDEPQGNQVFAPFKETMILVADAMRRAQDETGAPKLFSANITADDPAEMIARGEFILKTFGE..NASHVAFLVDGFVAGPTAVTTCRRNFPGTFLHYHRAGHGAVTSRQSQRGYTVLVHMKMARLIGASGIHTGTMGYGKMEGAPDEKMVAYMLERQMADGSHYRQDWGGMMACTPIISGGMNALR.................................................................................... [uniref90|F5BZE3 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II (Fragment) n=3 Tax=Alphaproteobacteria RepID=F5BZE3_9PROT]
F2ZCC9  : ......................................................................................................................GNNQGMGDVKCAQMVDFHVPKQMLDIFDGPATDITDLWNTLGRPRENGGYIAGTIIKPKLGLRPKPFAEAAYQFWLGGDFIKNDEPQGNQVYARMKDVTPLVSDAMKRAQDETGEAKLFSANITADDHHEMCARADYILEAFGE..NAHHVAFLVDGYVGGCGMVTTARRNYPDQYLHYHRAGHGAITSPSSVRGYTAFVLAKLSRLMGASGIHVGTMGYGKMEGGKDDRNIAYMIEQDSADGPFFHQEWYGMKPTTPIISGGMNALR.................................................................................... [uniref90|F2ZCC9 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=8 Tax=uncultured bacterium RepID=F2ZCC9_9BACT]
F2ZCF1  : ......................................................................................................................GNNQGMGDVEYGKMHDFYVPPAYLRLFDGPSTTISDLWRVLGRPVVDGGFIVGTIIKPKLGLRPQPFADAAYQFWLGGDFIKNDEPQGNQLFAPMKETIPLVADAMRRAQDETGEAKLFSANITADDPFEIIARGEYILETFAE..NADHVAFLVDGYVTGPAAITTARRRFPDQYLHYHRAGHGAVTSPQSMRGYTAFVLSKMARLQGASGIHTGTMSFGKMEGEAGDTDMAYMIQDDSADGPFYHQEWLGMNPTTPIISG.......................................................................................... [uniref90|F2ZCF1 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=3 Tax=uncultured bacterium RepID=F2ZCF1_9BACT]
F2ZCD7  : ......................................................................................................................GNNQGMGDVQCAQMQDFWVPKQMLDIFDGPATDITDLWNLLDRPRENGGYIAGTIIKPKLGLRPKPFAEAAYQFWLGGDFIKNDEPQGNQKYARMKDVTPLVADAMKRAQDETGEAKIFSANITADDHHEMIARADYILEAFGE..NANHVAFLVDGYVGGCGMVTTARRNYPDQYLHYHRAGHGAITSPSSVRGYTAFVLGKLSRLMGASGIHVGTMGFGKMEGGNEDKIICYMLEREECQGPFFFQKWYGMKPTTSII............................................................................................ [uniref90|F2ZCD7 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=1 Tax=uncultured bacterium RepID=F2ZCD7_9BACT]
Q6ST42  : .......................................................................................................................NNQGMGDVEYAKMHEFYVPEAYRALFDGPSVNISALWKVLGRPEVDGGLVVGTIIKPKLGLRPKPFAEACHAFWLGGDFIKNDEPQGNQPFAPLRDTIALVADAMRRAQDETGEAKLFSANITADDPFEIIARGEYVLETFGE..NASHVAFLVDGYVAGAAAITTARRRFPDNFLHYHRAGHGAVTSPQTKRGYTAFVHCKMARLQGASGIHTGTMGFGKMEGESSDRAIAYMLTQDEAQGPFYRQSWGGMKACTP.............................................................................................. [uniref90|Q6ST42 Form II ribulose-1,5-bisphosphate carboxylase/oxygenase (Fragment) n=1 Tax=Rhodospirillum rubrum RepID=Q6ST42_RHORU]
F2ZCG2  : ......................................................................................................................GNNQGMGDVEYAKMYDFFISPSAIELFDGPVKGISDLWRILGRPLIDGGLIVGTIIKPKLGLRPQPFADAAYQFWLGGDFIKNDEPQGNQVFAPMKDVIPLVVDTMKRVQDETGDAKLFSANITADSHDEMIARGEYILGQFGEY..ADHCAFLVDGYVGGPGMVTTARRWFPDQYLHYHRAGHGAITSPQSQRGYSAYVLAKMARLQGASGIHVGTMGFGKMESEPKDRNIAYLIERQSFDGPAYHQEWGGMKPTTPIISGGMNALR.................................................................................... [uniref90|F2ZCG2 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=1 Tax=uncultured bacterium RepID=F2ZCG2_9BACT]
F2ZCF0  : ......................................................................................................................GNNQGMGDVKEAKIYDFWIPPKFLQLFDGPSMDISDMWRTLGRPLKDGGYIAGTIIKPKLGLRPEPFADAAYQFWLGGDFIKNDEPQGNQTFCPMKKVLPLVADAMKRAQDETGEAKLFSANITADDHYEMLARADYVLETFAE..NASHVAFLVDGFVGGPGMITTARRNYPNQYLHYHRAGHGMITSPSAKRGYDAYVLGKLARLQGASGIHVGTMGYGKMEGSQADKIICYMLERDECQGPLY.......................................................................................................... [uniref90|F2ZCF0 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=1 Tax=uncultured bacterium RepID=F2ZCF0_9BACT]
F2ZCE8  : ..................................................................................................................................KMHDFYVPPAMLQLFDGPAKDISDLWRVLGRPIQDGGFIVGTIIKPKLGLQPKPFADAAYDFWLGGDFIKNDEPQGNQVFAPMKKTIPLVADSMKRAQDKTGEAKLFSANITADDPFEIIARGEYVLEQFGE..NANHVAFLIDGYVGGPTAITTARRVFPNQYLHYHRAGHGAVTSPSAKRGYTAFVLSKMARLQGASGIHTGTMSFGKMEGEKGDTDMAYMIERDVARGPVYQQEWLGMKPTTPIISGGMNALR.................................................................................... [uniref90|F2ZCE8 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=1 Tax=uncultured bacterium RepID=F2ZCE8_9BACT]
F2ZCE9  : .....................................................................................................................................DFYVPPDFLRLFDGPATTISNLWRVLGRPHQNGGFIVGTIVKPKLGLRPRPFADACYDFWLGGDFIKNDEPQGNQTFSPLKETIPLVADAMRRAQDETGEAKLFSANITADDHYEMVARGEFILDTFGEF..ADHVAFLVDGYVAGAAAVTTARRSFPQQYLHYHRAGHGAITSPQSKRGYTAFVHCKMARLQGASGIHTGTMSFGKMEGEAADRAIAFMLEQDSADGPYFHQEWHGMNPTTSIISG.......................................................................................... [uniref90|F2ZCE9 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=1 Tax=uncultured bacterium RepID=F2ZCE9_9BACT]
C0KTR3  : ..................................................................................................................................KMLDFYVPPKYLRLFDGPSKDISDMWRILGRPIKDGGYIAGTIIKPKLGLRPEPFAQAAYQFWLGGDFIKNDEPQGNQVFCPAKKVYPLVYDAMKRAMDETGQAKLFSANITADDHYEMVARGEFILETFGP..DADKVAFLVDGYVGGPGMVTTARRVFPNQYLHYHRAGHGAVTSPSAKRGYTAFVLAKMSRLQGASGIHVGTMGYGKMEGEADDRNIAYMIERDSADGPFFHQEWEGMKPTTPIIS........................................................................................... [uniref90|C0KTR3 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II (Fragment) n=1 Tax=marine magnetite-containing magnetic spirillum MMS-1 RepID=C0KTR3_9PROT]
F2ZCE6  : ..................................................................................................................................KMYDFWFPPEYLRLYDGPATDISDMWRVLGRPVVNGGFIVGTIIKPKLGLRPQPFARAAYDFWLGGDFIKNDEPQGNQVFAPLKETITAVADSMRRAQDDTGEAKLFSANITADDYREIIARGEFILETFAE..NADHVAFLIDGYVAGPAAITTARRYFPNQYLHYHRAGHGAVTSPQTQRGYTSFVLAKMARCQGASGIHVGTMGYGKMEGEMDDRAIAYMIERDSADGPFFHQEWQGMKPTTPIVSG.......................................................................................... [uniref90|F2ZCE6 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=1 Tax=uncultured bacterium RepID=F2ZCE6_9BACT]
F3KC42  : LDQSYRYVNLDLDEDQLIKLGRHVLVAYIMRPKTGFDFLATAAHFAAESSTGTNVEVCTTDDHTRSVDALVYHAD.........KKTGLVKIAFPIDLFDRNIIDGKAMVASFLTLCIGNNQGMGDVEYGKMHDFYFPPEYLKLYDGPATTLSHFWKILGRREQHGGLIVGTIIKPKLGLRPEPFAKAAYDFWLGGDFIKNDEPQGNQPFAPLKETITLTSGSLRRAQDKTGEAKLFSANITADDHDEMLARGEFILDAFKE..NADHVAFLVDGYVAGPSAVTNGPQKF.................................................................................................................................................................................... [uniref90|F3KC42 Ribulose bisphosphate carboxylase n=1 Tax=gamma proteobacterium IMCC2047 RepID=F3KC42_9GAMM]
D0ETF9  : ........................................................................................................................................VPPTYLQLFDGPASNVSDLWRALGRDPYNGGFVVGTIIKPKLGLRAQPFADAAYDFWLGGDFIKNDEPQGNQTFAPMRETIPKVVDAMKRAQDETGQAKLFSANITADDPFEVIARGEYILEQFGEF..AHHVAFLVDGYVAGPTAITTARRRFPNQFLHFHRAGHGAVTSPQTERGYSAFVLSKMSRLQGASGIHTGTMGFGKMEGDAADKAIAYMLERDEAEGPYFKQNWYGTKATT............................................................................................... [uniref90|D0ETF9 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II (Fragment) n=3 Tax=Gammaproteobacteria RepID=D0ETF9_9GAMM]
Q41407  : LEQSSRYADLTLDEAGSLRNGEHVLVAYIMKPKMGYDYLATAAHFAAESCTGAR....STDDAKESANAVVYYIDADSQE.........MRIAYPTVLFDSNLTDGRDMVRSFLTLAIGNTQGMEDVEFGKIYDFYLPPSFLRLQESPSVN..TMWRILDKGASNGGLAAGAM.KPKLGMQPKPFRAASYALWQGGAYTTADV.QANQAPTQASEGIPEVVKAMRSCVQGTDVAKRHSGGNYTDEPKEMDARGKYVLSQFGPFSG..NCVSLVAGYAAGGS....ARHTFPRQFVHYHRAGQASTSSPQTQRGYSAFVHTKISQVISTTSIHADTMSFGKTQGDSPDKSIAVMLQDDAADARLCNQEWEGMRQNAPIISGSMNALRLPAFFETLGNSNVILTADSGSFGHKDGPASGAIACRQAWKAWRSGSDVVEFAKTHEEIKGAFLTFPKDADEIYPGWKEKLG... [uniref90|Q41407 Uncharacterized ribulose bisphosphate carboxylase-like protein (Fragment) n=1 Tax=Symbiodinium sp. RepID=RBLL_SYMSP]
UPI00003: ...........................................................................................................................................................................................................................MADAMPRAQDERACPSCFSANITADDPAEMIARGNFILETFGE..NASHVAFLVDGFVAGPTAVTTCRRNFPDTFLHYHRAGHGAITSRQSKRGYTVLVHMKMARLLGASGIHTGTMGYGKMEGAPDEKMVAYMLERQIAEGPYYRQDWGGMASCTPIISGGMNALRLPGFFDNLGHSNVIQTSGGGAFGHKDGAIAGALSLRQAHEAWLKKIDLVDYAQTHAELRGAFESFASDADRLYPGWRDRLRI.. [uniref90|UPI0000383BB2 COG1850: Ribulose 1,5-bisphosphate carboxylase, large subunit n=1 Tax=Magnetospirillum magnetotacticum MS-1 RepID=UPI0000383BB2]
D0ETF4  : ..............................................................................................................................................RLFDGPAMNIQDMWGVVGRDINNGGMVVGTIIKPKLGLRPQPFADACYQFWLGGDFIKNDEPQGNQVFAPLKKTIPLVADAMKRAQDETGEAKIFSANITSDDPFEMIARGEFILETFGE..NADHVAFLVDGFVGGPMAVTTCRRYFANQFLHYHRAGHGMVTSPQTQRGYNALVHMKMSRMQGASGIHTGTMGFGKMEGDPTDKLLAYMLENEEAEGLYYPQKWYGMKPTTP.............................................................................................. [uniref90|D0ETF4 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II (Fragment) n=3 Tax=Thiohalomonas RepID=D0ETF4_9GAMM]
D0ETE9  : .............................................................................................................................................IELFDGPSKDISDMWRILGRPIVDGGYIAGTIIKPKLGLRPEPFAQAAYQFWLGGDFIKNDEPQGNQTFAPIKKVMPLVADAMKRAQDETGEAKLFSANITADDHFEMCARADFILETFGE..DADKVAFLVDGYVGGPGMITTARRQYPSQYLHYHRAGHGAVTSPSAKRGYTAFVLAKMSRLQGASGIHVGTMGYGKMEGGKDDRNIAYMIERDSADGPVYHQEWYGMK.................................................................................................. [uniref90|D0ETE9 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II (Fragment) n=3 Tax=Halothiobacillus RepID=D0ETE9_9GAMM]
F2ZCE1  : ..................................................................................................................................KMIDFYMPPRVIQMFDGPARDISDLWRVLGRPHVDGGFIVGTIVKPKLGLRPKPFADAAYEFWLGGDFIKNDEPQGNQLFAPMKETIPLVADAMRRAQDETGEAKLFSANITADDHYEMVARGEYILETFAE..NADHVAFLVDGYVTGPAAITTARRRFPSQYLHYHRAGHGAVTSPQTKRGYTAFVLSKMARMQGASGIHTGTMSYGKMEGEASDTDMAYMIQQDSADG............................................................................................................. [uniref90|F2ZCE1 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=2 Tax=uncultured bacterium RepID=F2ZCE1_9BACT]
Q933G7  : ........................................................................................................................................VPPAYLRLFDGPSTTIKDLWRVLGRPVVDGGFIVGTIIKPKLGLRPQPFADACYDFWLGGDFIKNDEPQGNQVFAPFKDTVRAVNDAMRRAQDATGQPKLFSFNITADDHYEMLARGEYILETFGE..NADHVAFLVDGYVAGPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHVGTMGYGKMEGEASDRDSAFMITQDSAEGPYFKQEW...................................................................................................... [uniref90|Q933G7 Form II ribulose 1,5-bisphosphate carboxylase/oxygenase (Fragment) n=5 Tax=Rhodopseudomonas palustris RepID=Q933G7_RHOPA]
E2CZG6  : ..................................................................................................................................QMIDFFMPPRAIQLFDGPAKDISDLWRILGRPIKDGGYIAGTIIKPKLGLRPEPFAAAAYQFWLGGDFIKNDEPQGNQVFAPVKKTIPLVYDAMKRAMDETGEAKLFSMNITADDHYEMCARADFALETFGP..DADKLAFLVDGFVGGPGMITTARRQYAGQYLHYHRAGHGMITSPSAKRGYTAFVLAKMSRLQGASGIHVGTMGYGKMEGGADDRNIAYMIERDSCDGPVYHQEWYGM................................................................................................... [uniref90|E2CZG6 Ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit type I (Fragment) n=1 Tax=Acidithiobacillus ferrooxidans RepID=E2CZG6_THIFE]
F2ZCB8  : ..................................................................................................................................KMIDFWVPRRVIELFDGPAKDISDLWRILGRPVKDGGYIAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEPQGNQVFAPMKKVMPLVADAMRRAQDETGEAKLFSANITADDHNEMVARGEYILETFAE..NADHVAFLVDGFVGGPGMVTTARRWFPNQYLHYHRAGHGMVTSPSSKRGYTAFVLAKMSRLQGASGIHVGTMGYGKMEGDADDRIIAY...................................................................................................................... [uniref90|F2ZCB8 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=1 Tax=uncultured bacterium RepID=F2ZCB8_9BACT]
Q5DVV4  : ............................................................................................................................................................................IIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEPQGNQVFCPIKKVLPLVHDAMKRAQDETGEAKLFSMNITADDYHEMCARADFALETFGE..DAPRLAFLVDGYVGGPGMVTTARRQYPNQYLHYHRAGHGAVTSPSSKRGYTAYILAKMSRLIGASGIHVGTMGYGKMEGSTDDTIIAYMIERDECQGPVYYQKWYGMKPATPIISGGMNA...................................................................................... [uniref90|Q5DVV4 Ribulose-1,5-bisphosphate carboxylase oxygenase large subunit (Fragment) n=2 Tax=uncultured prokaryote RepID=Q5DVV4_9ZZZZ]
Q5DVU3  : ............................................................................................................................................................................IIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEPQGNQVFAPMKKVIPLVADAMKRAQDETGQAKLFSANITADDHDEMIARGEYILETFGEF..ADHVAFLVDGYVGGPGMVTTARRWFPNQYLHYHRAGHGAVTSPSSKRGYTAYVLAKMSRLQGASGIHVGTMGYGKMEGDKDDRAIAYIIERDEYQGPAYNQKWYGMKPTTPIISGGMNA...................................................................................... [uniref90|Q5DVU3 Ribulose-1,5-bisphosphate carboxylase oxygenase large subunit (Fragment) n=1 Tax=uncultured prokaryote RepID=Q5DVU3_9ZZZZ]
Q5DVU1  : ............................................................................................................................................................................IIKPKLGLRPEPFAEAACQFWLGGDFIKNDEPQGNQVFCPMKKVIPLVADALARAQDETGEAKLFSANITADDRHEMCARADYILETFGE..NASHVAFLVDGYIGGPGMVTTARRNYPGQYLHYHRAGHGAVTSPSSKRGYTAYILAKMSRLMGASGIHVGTMGYGKMEGDASDKIIAYMIERDECQGHVYYQKWYGMRPTTPIITGGMN....................................................................................... [uniref90|Q5DVU1 Ribulose-1,5-bisphosphate carboxylase oxygenase large subunit (Fragment) n=1 Tax=uncultured prokaryote RepID=Q5DVU1_9ZZZZ]
F2ZCD4  : ..................................................................................................................................KLLDFFVPPNFLRLFDGPSKGIQDMWRILGRPLENGGMVVGTIIKPKLGLRPKPFADACYQFWLGGDFIKNDEPQGNQVYAPMRESIPLVVDAMKRAMDETGQGKIFSANITADSHDEMLARGEYVLEQFG..GMAENVALLVDGFVGGTGMVTTARRHFSNQFIHYHRAGHGMVTGEESNRGYTALAHMKWARMAGSSGIHTGTMGFGKMEGYNSDTVLADVLIDDVSVGTHYTQPWERMKPTAPIISG.......................................................................................... [uniref90|F2ZCD4 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=1 Tax=uncultured bacterium RepID=F2ZCD4_9BACT]
D5EB97  : ......YVNLELPDPT...NGEYLLTVFRLVPGGEMNMLQAAAEIAAESSTGTNFRVNTETKFSKVMNALVYQMDLER.........ELVWIAYPWRLFDRG.....GNVQNILTYIVGNVLGMKEISALKLLDVWFPPSMLEQYDGPGFTVDDMRSYLGVYDRP...ILGTIVKPKMGLTSAEYAEVCYDFWAGGDFVKNDEPQANQDFCPYDKMVKHVKEAMDKAVKETGKKKVHSFNVSAPDFDTMIERCEMIRN..AGFEPGSY.AFLIDGITAGWMAVQTIRRRYPDVFLHFHRAAHGAFTRPENPIGFSVLVLSKFARLAGASGIHTGTAGVGKMKGTPEEDVVAHGIQYLSSHGHFFDQSWRGMKKCCPIVSGGLNPVRLKPFIDVMGNVDFITTMGSGVHAHPEGTRSGAKALIQACDAYLQGIDIKDYAKNHRELEQAIEFFPE................. [uniref90|D5EB97 Ribulose-bisphosphate carboxylase n=1 Tax=Methanohalophilus mahii DSM 5219 RepID=D5EB97_METMS]
Q12TQ0  : ...SKQQAYVDLKLPDPT.NGEFLLAVFHMIPGGDLNVLQAAAEIAAESSTGTNIKVSTETAFSRTMNARVYQLDLER.........ELVWIAYPWRLFDRG.....GNVQNILTYIIGNILGMKEIQALKLMDIWFPPSMLEQYDGPSYTVDDMRKYLDVYDRP...ILGTIVKPKMGLTSAEYAEVCYDFWVGGDFVKNDEPQANQDFCPYEKMVAHVKEAMDKAVKETGQKKVHSFNVSAADFDTMIERCEMI..TNAGFEPGSY.AFLIDGITAGWMAVQTLRRRYPDVFLHFHRAAHGAFTRQENPIGFSVLVLSKFARLAGASGIHTGTAGIGKMKGPAEDVVAAHSIQYLKSPGHFFEQSWRAMKKCCPIVSGGLNPVKLKPFIDVMENVDFITTMGSGVHSHPGGTQSGAKALVQACDAYLQGMDIEEYAKDHKELAEAIEFY................... [uniref90|Q12TQ0 Ribulose-1,5-bisphosphate carboxylase-oxygenase type III n=1 Tax=Methanococcoides burtonii DSM 6242 RepID=Q12TQ0_METBU]
Q5DVV5  : ............................................................................................................................................................................IIKPKLGLRPKPFAEACYNFWLGGDFIKNDEPQGNQIWGPIKEVVPLVKDSLVRAQDDTGMAKLFSFNITADDHYEMLHRGEYILETFAEFSE..NIAFLVDGCVGGPGMVTTARRNFPDQFLHYHRAGHGAVTSDQSDRGYNMLVHMKMARLQGASGIHTGTMGYGKMEGAADDKVIAYMLERDSADGLSYHQEWEGMKATTPIICGGMNA...................................................................................... [uniref90|Q5DVV5 Ribulose-1,5-bisphosphate carboxylase oxygenase large subunit (Fragment) n=11 Tax=uncultured prokaryote RepID=Q5DVV5_9ZZZZ]
F4BTL5  : ..................RNGEYLLAVFHLIPSGELNIMQAAAEVAAESSTGTNFAVKTETPFSRVMNALVYKVDIEK.........NLVWIAYPWRLFDRN.....GNVQNIMTYIAGNALGMKEIKALKLLDIWFPPSMLEQYDGPSYTLDDMRTYLNVHDRP...ILGTIIKPKMGLTSSEYAEVCYDFWVGGDFVKNDEPQADQDFCPYDKMVKYVKMAMDKAVKETGKKKVHSFNVSSADFDTMIERCEMIRE..AGFEPGSY.AFLIDGITAGWMAVQTLRRRYPDVFLHFHRAGHGGFTRPENPIGFSVLVLSKFARLAGASGIHTGTAGVGKMAGSPEEDVTAARILKVEGKGHFFTQSWRGLKKCCPIISGGLNPTLLEPFIDVMGGIDFITTMGAGCHAHPRGTRAGAMALVQACEAYKNKIDIADYAKDHRELAEAIEFFSKKKKK............. [uniref90|F4BTL5 Ribulose bisphosphate carboxylase, large chain (Form II) n=1 Tax=Methanosaeta concilii GP-6 RepID=F4BTL5_METSO]
Q75NW2  : ............................................................................................................................................................................IIKPKLGLRPKPFADACYDFWLGGDFIKNDEPQGNQLFAPLKETIPLVADAMKRAQDKTGEAKLFSANITADDHYEMLARGEFILETFG..GNADHVAFLVDGYVTGPAAITTARRAFPKQYLHYHRAGHGAVTSPSAMRGYTAFVLSKMARMQGAYGIHTGTMGFGKMEGEAADKLMAYMIMDDSADGPYYHQEWQGMGQTTPIITGGMNA...................................................................................... [uniref90|Q75NW2 Ribulose,1-5,bisphosphate carboxylase oxygenase form II large subunit (Fragment) n=1 Tax=uncultured prokaryote RepID=Q75NW2_9ZZZZ]
F2ZCB3  : ......................................................................................................................GNNQGMGDVEYAKLLDFYVPPRFLRLFDGPSMNIVDMWRILGRDLDNGGMVVGTIIKPKLGLRSQPFADACYQFWLGGDFIKNDEPQGNQVYAPMREITPLVADAMKRAMDETGQPKLFSANITADDPFEMIARGEYILETFGEH..AENVAFLVDGYVGGCGMVTLARRYFPKQFLHYHRAGHGAVTSEESNRGYTALVHMKWARMSGASGIHVGTMGYGK.................................................................................................................................. [uniref90|F2ZCB3 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=2 Tax=uncultured bacterium RepID=F2ZCB3_9BACT]
Q5DVU4  : ............................................................................................................................................................................IIKPKLGLRPRPFADASYDFWLGGDFIKNDEPQGNQVFAPMSETIPLVADAMRRAQDKTGEAKLFSSNITADDPFEMIARAEFILDTFAE..NANHVAFLVDGYVAGPAAISTARRQFPAQYLHYHRAGHGAFTSPQSDRGYTAFVLGKLSRLMGASGIHVGTMGYGKMEGEHDDRNIAYMINDDSADGPFYHQEWLGIKPTTPIISGGMNA...................................................................................... [uniref90|Q5DVU4 Ribulose-1,5-bisphosphate carboxylase oxygenase large subunit (Fragment) n=7 Tax=uncultured prokaryote RepID=Q5DVU4_9ZZZZ]
Q5DVU2  : ............................................................................................................................................................................IIKPKLGLRPKLFADACYQFWLGGDFVKNDEPQGNQVFAPLKETIRLVADAMKRAQDETGEAKLFSANITADDPFEMIRRGEYILETFGE..DADHVAFLVDGFVGGPSAVATARRQFPNQFLHYHRAGHGMVTSERTNRGYNLLTHMKWSRLLGASGIHTGTMGYGKMEGKPEDKLVAFMLTEDEADGLFYRQPWWKMKATTPIISGGMNA...................................................................................... [uniref90|Q5DVU2 Ribulose-1,5-bisphosphate carboxylase oxygenase large subunit (Fragment) n=2 Tax=uncultured prokaryote RepID=Q5DVU2_9ZZZZ]
F2ZCC1  : ..................................................................................................................................QMQDFYIPPKMLQLFDGPSKDISDLWRILGRPVENGGYIAGTIIKPKLGLRPKPFADAAYSFWLGGDFIKNDEPQGNQLFCPIKEVLPLIADSLARAQDETGEAKLFSMNITADDYHEMCARADYALETFGE..NATHLAFLVDGFVGGPGMVTTARRQYPDQYLHYHRAGHGMITSPSSKRGYTAYILAKMSRLMGASGIHVGTMGYGK.................................................................................................................................. [uniref90|F2ZCC1 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=1 Tax=uncultured bacterium RepID=F2ZCC1_9BACT]
D0ETG0  : ..............................................................................................................................................................LGRDSYNGGFVVGTIIKPKLGLRAQPFADAAYDFWLGGDFIKNDEPQGNQTFAAMRETIPKVVDAMKRAQDETGQAKLFSANITADDPFEVIARGEYILEQFGEF..AHHVAFLVDGYVAGPTAITTARRRFPNQFLHFHRAGHGAVTSPQTERGYSAFVLSKMSRLQGASGIHTGTMGFGKMEGDAADKAIAYMLERDEAEGPYF.......................................................................................................... [uniref90|D0ETG0 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II (Fragment) n=1 Tax=Thiohalospira halophila RepID=D0ETG0_9GAMM]
Q75NV6  : ............................................................................................................................................................................IIKPKLGLRPKPFAEAAYQFWLGGDFIKNDEPQGNQVLSRMKEVTPFGCDAMARAQDETGEAKLFSANITADDHHEMCARADYILETFAE..NAHHVAFLVDGYVGGCDMVTTARRNYPGQYLHYHRAGHGAITSPSAVRGYTAFVLAKLSRLMGASGIHVGTMGYGKMEGGADDRNIAYMIERDSADGPFYHQEWFGMKPTTPIISGGMNA...................................................................................... [uniref90|Q75NV6 Ribulose,1-5,bisphosphate carboxylase oxygenase form II large subunit (Fragment) n=3 Tax=uncultured prokaryote RepID=Q75NV6_9ZZZZ]
Q08EW4  : .......................................................................................................................NNQGMGDIEHAKIHDFYMPERATQLFDGPSKDISDMWRILGRPVKDGGYNAGTIIKPKLGLRPEPFAQAAYQFWLGGDFYKNDEPQGNQVFSPMKKTMPLVVDAMKRAHSETGQAKLFFTNITADDHYEMCARADFILEAFGP..DADKVAFLVDGYVGGPGMITTARRQYGNQYLHYPRAGHGAVTSPSAKRGYTAFVLAKMSRYQGASGAHVGTMGYGKME................................................................................................................................ [uniref90|Q08EW4 Ribulose 1,5-bisphosphate carboxylase/oxygenase large subunit (Fragment) n=12 Tax=uncultured marine bacterium RepID=Q08EW4_9BACT]
Q08EW6  : .......................................................................................................................NNQGGGDIEHAKIHGIYMPERAIQLFDGPSKDISDMWRILGRPVKDGGYNAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEIQGNQVFSPMNQTIPLVVDAMKRAQDETGQAKLFSANITADDQYEMCARADFILEAFGP..DADKVAFLVDGYVGDPGMITTARSQYPNQYLHYHRAGHGAVNSPKIKRGYTAFVLAKMSRLQGASGAHVGTMGYGKME................................................................................................................................ [uniref90|Q08EW6 Ribulose 1,5-bisphosphate carboxylase/oxygenase large subunit (Fragment) n=1 Tax=uncultured marine bacterium RepID=Q08EW6_9BACT]
F5BZE0  : ...............................................................................................................................................................................................FWLGGDFIKNDEPQGNQVFAPLKETMRLVADAMKRAQDETGQAKLFSANITADDPAEMLARGHYILETFAE..NASHVAFLVDGYVAGPTAVTTCRRNFPGQFLHYHRAGHGAVTSSQSKRGYTVLVHMKMARLIGASGIHTGTMGYGKMEGDPSEKMVAYMLERDQADGPYYRQDWCGMKSCTPIISGGMNA...................................................................................... [uniref90|F5BZE0 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II (Fragment) n=1 Tax=alpha proteobacterium LEMS RepID=F5BZE0_9PROT]
Q08EX8  : .......................................................................................................................NNQGMGDIEHAKIHDFYMPERAIQLFDGPSKDISDMWRILGRPVKDGGYNAGTIIKPELGPRPEPFAQAAYQFWLGGDFIKNDEPQGNQVFSPMKKTVPLVADAMNGAQDETGQARLFSANITADDHYEIGARARFILDPFGPDDDK..VAFLVDGYVGGPGMITTAHRQYPNQYLLYHRAGHGAVTSPSAKRGYTAFVLAKMSRLQGASGAHVGTMGYGKME................................................................................................................................ [uniref90|Q08EX8 Ribulose 1,5-bisphosphate carboxylase/oxygenase large subunit (Fragment) n=1 Tax=uncultured marine bacterium RepID=Q08EX8_9BACT]
F2ZCC5  : ..................................................................................................................................QMFDFYMPPYMLSLFDGPAKSINDLWALLGRDYNDGGYIAGTIIKPKLGLRPQPFADAAYQFWLGGDFIKNDEPQGNQVFCPVKEVMPLIADAMKRAEDETGEAKLFSANITADDYHEMCARADFILETFGE..DAPRVAFLVDGYVGGPGMVTTARRQYPSQYLHYHRAGHGAVTSPSSKRGYTAYILAKMSRLMGASG............................................................................................................................................ [uniref90|F2ZCC5 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=1 Tax=uncultured bacterium RepID=F2ZCC5_9BACT]
Q08EW5  : .......................................................................................................................NNQGMGDIEHAKIRDFYMPKRAIQLFDGPSKGISDMWRILGRPVKDGGYNAGTIIKPKLGLRPEPFAQAAYQFWLGGDFIRVDEPQGNQVFSPMKATIPLVVDAMKRAHDETGQAKRFSANITADDHYEMCARADFIMEAFGP..DADKVSFLVGEYVGGPGMITTARRQYPNQYLHYHRAGQSAITSPSAKRGYTAFVLAKMSRLQGASGAHVGTWGYGKME................................................................................................................................ [uniref90|Q08EW5 Ribulose 1,5-bisphosphate carboxylase/oxygenase large subunit (Fragment) n=1 Tax=uncultured marine bacterium RepID=Q08EW5_9BACT]
F2ZCB0  : ......................................................................................................................GNNQGMGDIAYAKMIDFYMPPRAIQLFDGPAKDISDLWRMLGRPVVDGGYISGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEPQGNQVFAPIKQVLPLVADAMKRAQDETGEAKLFSMNITADDHFEMCARADFALEAFGE..DADKVAFLVDGFVGGPGMITTARRQYPNQYLHYHRAGHGMVTSPSAKRGYTAFVLAKM.................................................................................................................................................... [uniref90|F2ZCB0 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=1 Tax=uncultured bacterium RepID=F2ZCB0_9BACT]
F2ZCC8  : ......................................................................................................................GNNQGMGDIAYAKMIDFYMPPRAIQLFDGPAKNIVDMWRILGRPIENGGYIAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEPQGNQTFAPIKKTLPLVYDSMKRAQDETGQAKLFSLNITADDHYEMCARADFGLETFGP..DADKLAFLVDGFVGGPGMVTTARRQYPNQFLHYHRAGHGMITSPSAKRG............................................................................................................................................................. [uniref90|F2ZCC8 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=1 Tax=uncultured bacterium RepID=F2ZCC8_9BACT]
A1L0Q1  : .................................................................................................................................................................................................................FCQMNECIPEVVKAMRAXIKETGXGKLFSANITADDPNEMIARGKYCLSQFGPLSE..NCAFLVDGYVAGGTAVTCARRNFPXQFLHYHRAGHGSVTSPQTQRGYTAFVHTKISRVIGASGIHTGTMSFGKMEGDASDKNIAFMLQDDAADGPYYXQEWEGMKQTTPIISGGMNALRLPAFFENLGHSNVILTAGGGAXGHKXGPKPGAXSXRQAWKXWKSGSDVIEFAKTHEE........................... [uniref90|A1L0Q1 Chloroplast ribulose 1,5-bisphosphate carboxylase oxygenase large subunit (Fragment) n=1 Tax=Symbiodinium sp. clade A ex Anemonia viridis RepID=A1L0Q1_9DINO]
UPI00003: MDQSKRYVNLALSEADLIKGGRHVLCAYRMRPRPGHGYVETAAHFAAESSTGTNVEVCTTDDFTRGVDALVYEVDEAE.........GLMKIAYPVDLFDRNIIDGKAMIASFLTLTVGNNQGMSDVENAKMEDFYVPPEFLKLFDGPACNISHMWKVLGRPEVNGGMVVGTIIKPKLGLRPNAFDECWHQFWMGGESIR.............................................................................................................................................................................................................................................................................. [uniref90|UPI0000383C47 COG1850: Ribulose 1,5-bisphosphate carboxylase, large subunit n=1 Tax=Magnetospirillum magnetotacticum MS-1 RepID=UPI0000383C47]
D9J1W4  : .............................................................................................................................................................................................................................................................................ALLVDGFVAGPTAVATARRNFPRQWLHYHRAGHGMITSPQTQRGYTALVLSKFSRLLGSSGIHVGTMGFGKXESEASDRDIVYMLERDVAKGPYFTQQWANMNPTTGIISGGMNAIRMVNFFTNLGHANVVMTCGGGSYGHVDGPSEGAKSCRQAWLCWKEGADPLEFAKENRQYARAFISFAADSDQIYPTWRKGL.... [uniref90|D9J1W4 Plastid ribulose-1,5-bisphosphate carboxylase oxygenase (Fragment) n=1 Tax=Chromerida sp. RM11 RepID=D9J1W4_9ALVE]

6. The initial homology models

For each of the templates listed above, models were built. Either a single model if the alignment was certain, or a number of alternative models if the alignment was ambiguous.

6.1. Homology model 1/15, based on template 7T1C-~, alignment variant 01

This model is a homodimer, and based on the following profile-profile alignment:

(To improve readability, only up to ten lines of the complete target multiple sequence alignment (MSA) shown above are also displayed here (upside down). The template MSA has been shrunk and focused on structurally aligned PDB entries. The actual target-template alignment can be found in the middle at the line named 'Match'.)

Q08EW6  : .......................................................................................................................NNQGGGDIEHAKIHGIYMPERAIQLFDGPSKDISDMWRILGRPVKDGGYNAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEIQGNQVFSPMNQTIPLVVDAMKRAQDETGQAKLFSANITADDQYEMCARADFILEAFGP..DADKVAFLVDGYVGDPGMITTARSQYPNQYLHYHRAGHGAVNSPKIKRGYTAFVLAKMSRLQGASGAHVGTMGYGKME................................................................................................................................ [uniref90|Q08EW6 Ribulose 1,5-bisphosphate carboxylase/oxygenase large subunit (Fragment) n=1 Tax=uncultured marine bacterium RepID=Q08EW6_9BACT]
Q5DVV5  : ............................................................................................................................................................................IIKPKLGLRPKPFAEACYNFWLGGDFIKNDEPQGNQIWGPIKEVVPLVKDSLVRAQDDTGMAKLFSFNITADDHYEMLHRGEYILETFAEFSE..NIAFLVDGCVGGPGMVTTARRNFPDQFLHYHRAGHGAVTSDQSDRGYNMLVHMKMARLQGASGIHTGTMGYGKMEGAADDKVIAYMLERDSADGLSYHQEWEGMKATTPIICGGMNA...................................................................................... [uniref90|Q5DVV5 Ribulose-1,5-bisphosphate carboxylase oxygenase large subunit (Fragment) n=11 Tax=uncultured prokaryote RepID=Q5DVV5_9ZZZZ]
Q933G7  : ........................................................................................................................................VPPAYLRLFDGPSTTIKDLWRVLGRPVVDGGFIVGTIIKPKLGLRPQPFADACYDFWLGGDFIKNDEPQGNQVFAPFKDTVRAVNDAMRRAQDATGQPKLFSFNITADDHYEMLARGEYILETFGE..NADHVAFLVDGYVAGPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHVGTMGYGKMEGEASDRDSAFMITQDSAEGPYFKQEW...................................................................................................... [uniref90|Q933G7 Form II ribulose 1,5-bisphosphate carboxylase/oxygenase (Fragment) n=5 Tax=Rhodopseudomonas palustris RepID=Q933G7_RHOPA]
F2ZCE9  : .....................................................................................................................................DFYVPPDFLRLFDGPATTISNLWRVLGRPHQNGGFIVGTIVKPKLGLRPRPFADACYDFWLGGDFIKNDEPQGNQTFSPLKETIPLVADAMRRAQDETGEAKLFSANITADDHYEMVARGEFILDTFGEF..ADHVAFLVDGYVAGAAAVTTARRSFPQQYLHYHRAGHGAITSPQSKRGYTAFVHCKMARLQGASGIHTGTMSFGKMEGEAADRAIAFMLEQDSADGPYFHQEWHGMNPTTSIISG.......................................................................................... [uniref90|F2ZCE9 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=1 Tax=uncultured bacterium RepID=F2ZCE9_9BACT]
F2ZCD0  : ......................................................................................................................GNNQGMGDIANAQMQDFYVPPAMLALFDGPAKSINDLWTLLGRDNENGGYIAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEPQGNQVFCPLKKVLPLVHDAMKRAQDETGEAKLFSLNITADDHYEMCARADFGLETFGE..DAPRLAFLVDGFVGGPGMVTTARRQYSSQYLHYHRAGHGMITSPSSKRGYTAYILAKMSRLMGASGIHVGTMGYGKMEGGADDKIIAYMIERDECQGPFYYQKWHGMKPTTPIVSGGM........................................................................................ [uniref90|F2ZCD0 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=4 Tax=uncultured bacterium RepID=F2ZCD0_9BACT]
F5BZE6  : ......................................................................................................................GNNQGMGDVEYAKMIDFYMARSLLTLFDGPAMNITDMWRVLGRPQVNGGMVVGTIIKPKLGLRPKPFADACYMFWMGGDFIKNDEPQGNQVFAPTREIIPLVAEAMERAQQETGEAKIFSANITADDPFEMIRRGEFILEAFGK..NASHVAFLVDGYVGGPSAVTLCRRYFPNQFLHYHRAGHGAVTSNQSKRGYTVLTHMKMSRLQGASGIHTGTMGYGKMEGDKNEKMVAYMIERDEAMGVYYNQPWHGMTATTPIISGGMNALR.................................................................................... [uniref90|F5BZE6 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II (Fragment) n=1 Tax=alpha proteobacterium LM-5 RepID=F5BZE6_9PROT]
Q9FPW1  : LDQSSRYADLSLDEATLVKNGKHVLVAYIMKPKAGYDYLATAAHFAAESSTGTNVNVCTTDDFTKSVDALVYYIDPDSEE.........MKIAYPTLLFDRNIIDGRGMMCSFLTLAIGNNQGMGDVEYGKIYDFYLPPSFLRLYDGPAVNVEDMWRILGKGTSNGGLVDGTIIKPKLGLQPNPFGEACYSFWQGGDFIKNDEPQGNQVFCQMNECIPEVVKAMRACVKETGSSKLFSANITADDPEEMIARGKYIMSQFGPLSE..NCAFLVDGYVAGGTAVTCCRRNFPKQFLHYHRAGHGSVTSPQTQRGYTAFVHTKISRVIGASGIHVGTMSFGKMEGDASDKNIAYMLQDDEADGPYYRQEWQGMKETTPIISGGMNALRLPAFFENLGHSNVILTAGGGSFGHKDGPKIGAISCRQGEEAWKSLSDVIEYAKTHEEIKGAFLTFQKDADQIYPGWKEKLG... [uniref90|Q9FPW1 Ribulose 1,5-bisphosphate carboxylase oxygenase large subunit n=1 Tax=Symbiodinium sp. RepID=Q9FPW1_SYMSP]
E6VVI6  : .DQTSRYVNFDLKEDQLIADGNHVLCAYIYKPANGYGNVEVAAHFAAESSTGTNVEVCTTDDFTKGVDALVYEVSDASNGDS......LMKIAYPVELFDRNIIDGRAMLASFLTLCIGNNQGMGDVAYAKMHDFYVPRQYLELFDGPSKNIADFWRMLGRPTENGGMIAGTIVKPKLGLRPKPFADACYHFWLGGDFVKNDEPQGNQVFAPLKETITAVADAMRRAQDETGEAKIFSANITADDPREMIARGEFILNAFGE..NASRVAFLVDGYVAGPTAITTARRNFPNQFLHYHRAGHGAVTSPQAKRGYTAFVLSKMSRLQGASGIHTGTMGFGKMEGEMADKSMAYMIEREEAQGPYFKQKWYGMKATTPMISGGMNALRLPGFFDNLGHSNICQTSGGGAFGHLDGPTAGALSLRQSHDAWIQGVNLLDYAKEHNELARAFESFPGDADRFYPTWRHQL.... [uniref90|E6VVI6 Ribulose-bisphosphate carboxylase n=1 Tax=Desulfovibrio aespoeensis Aspo-2 RepID=E6VVI6_DESAO]
Q8RTI1  : MDQSNRYADLSLKEDDLIKGGNHVLVAYLMKPKTGYGYLEAAAHFSAESSTGTNVEVSTTDDFTKGVDALVYEIDEAK.........EIMKIAYPVDLFDRNITDGRAMIVSFLTLAIGNNQGMGDIAYAKMLDFYVPQKYLRLFDGPSKDISDLWRILGRPVVNGGYIAGTIIKPKLGLRPKPFAEAAYQFWLGGDFIKNDEPQGNQVFSPMRETIPLVYDSMKRAMDETGEAKLFSANITADDHYEMMARGEFILNTFGP..DADKVAFLVDGYVGGPGMVTTARRHFANQYLHYHRAGHGAVTSPSAKRGYTAFVLAKMSRLQGASGIHVGTMGYGKMEGDATDKNIAYMIERDSADGPFYHQEWYGMKPTTPIISGGMNALRLPGFFENLGHANLINTSGGGSYGHIDSPAAGAISLRQAYECWQQGADPIEFAKEHKEFARAFESFPGDADTIFPGWREKLGVHK [uniref90|Q8RTI1 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II n=1 Tax=magnetite-containing magnetic vibrio RepID=Q8RTI1_9PROT]
Q0F2Z8  : MDQSNRYADLSLNEADLIAGGKHLLVAYKLIPAKGYGFLEVAAHIAAESSTGTNVEVSTTDDFTRGVDALVYDIDETAFGDEGVTGGGLMKVAYPVELFDPNLIDGHYNVSHMWSLILGNNQGMGDHEGLRMLDFMVPECMIRKFDGPSAGIADLWKVLGRPEVDGGYISGTIIKPKLGLRPEPFAKACLDFWLGGDFIKNDEPQANQPFCPMKVVIPKVAEAMDRAQQETGQAKLFSANATADYHGECVARGEYILSEFAKYGNEKHVAFLIDGFVTGPAGVTTARRAFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLARLQGASGIHTGTMGYGKMEGHGKETVLAYMLERDECMGHYFNQKWYGMKPTAPIISGGMNALRLPGFFENLGHGNVINTCGGGSFGHIDSPAAGGKSLDQAYDCWKSGTDPIEYAKTHGEFARAFESFPGDADKLYPGWRDKLGVHK [uniref90|Q0F2Z8 Ribulose-bisphosphate carboxylase n=1 Tax=Mariprofundus ferrooxydans PV-1 RepID=Q0F2Z8_9PROT]
SecStr  : CCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCEEECCCCCCHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCEEEECCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEECCCCCCHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCHHCCCCCCCEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHHHHCCCC [Secondary structure predicted by PsiPred]
Target  : MDQSNRYANLNLKEEDLIKNGKHLLVAYKLIPAKGHGFLEVAAHVAAESSTGTNVEVSTTDDFTRGVDALVYEIDETAFGDDPVKGGGLFKVAYPVELFDPNLTDGTYNISHMWSLILGNNQGMGDHQGLRMLDFLVPEMMVRKFDGPSANISNLWKVLGRSETDGGYIAGTIIKPKLGLRPEPFAKACYDFWLGGDFIKNDEPQANQPFCPMEVVMPKVAEAMDRAQQATGQAKLFSANITADYYKEMIHRGDFVLETFAKYNSASHVAFLVDGFVTGPAGVTTARREFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLVRLMGASGMHTGTMGYGKMEGHGKETVLAYMLERDECQGPYFYQKWYGMKATTPIISGGMNALRLPGFFQNLGHGNVINTCGGGAFGHIDSPAAGGISLGQAYDCWKSGSDPIEYAKTHKEFARAFESFPKDGDKLFAGWREKLGVHK
Match   :  DQSNRYANL:LKEEDLI::G|H|LVAY|| PA G|GFLEVAAH|AAESSTGT            GVDALVYEIDETAFGD:    GGL:K|AYPVELFD NL D  | |SHMWSL|LGNNQGMGDH GLRMLDF :PE:MVR:FDGP::NI::|W|VLGR   DGGYIAGTIIKPKLGLRPEPFAKACYDFWLGG FIKNDEPQANQ F:PM: V:P VAEAMDRAQQ TG|AKLFSANITAD|| EMI RG|||L: FAKY:: :HVAFLVDGFVTGPAGV:TAR: FP TFLHFHRAGHGA:TSYKSPMGMDPLCYMKL:RL:GASG:HTGTMGYGKMEGH: E VLAYMLERDECQGPYFYQKWYGMKATTPIISGGMNALRL GFF|NLGH:NVINTCGGG:FGHID:PAAGG SL QAY:CWK:G:DPIE|AK HKEFARAFESFP D:DKLF GWREKLG   
Template: .DQSNRYANLDLKEEDLINGGRHMLVAYRMKPAPGYGFLEVAAHIAAESSTGT............GVDALVYEIDETAFGDQ....GGLLKIAYPVELFDHNLIDDKHPVSHMWSLVLGNNQGMGDHLGLRMLDFYLPEVMVRNFDGPATNIEDMWRVLGRPTKDGGYIAGTIIKPKLGLRPEPFAKACYDFWLGGTFIKNDEPQANQTFAPMKKVIPLVAEAMDRAQQETGEAKLFSANITADFFGEMIARGEYILNEFAKYGNEDHVAFLVDGFVTGPAGVATARHYFPKTFLHFHRAGHGALTSYKSPMGMDPLCYMKLARLQGASGIHTGTMGYGKMEGHSDERVLAYMLERDECQGPYFYQKWYGMKATTPIISGGMNALRLIGFFENLGHANVINTCGGGSFGHIDGPAAGGKSLDQAYQCWKEGADPIEFAKEHKEFARAFESFPWDADKLFPGWREKLG...
SecStr  : .CHHHHHCTTTTHHHHHHHHCCCEEEEEEEECTTTTHHHHHHHHHHHHHCCCC............GCCCEEEEEETTTTTTT....CEEEEEEETTTTCCCCCCCCCCHHHHHHHHHHGGGGCCCCCEEEEEEEEECHHHHHHCCCCCCCCHHHHHHHHCCCCCCCCCEEEECCCCCCCCHHHHHHHHHHHHHHCCEEEEETTTTCCTTTTHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCHHHHHHHHHHHHHHHHHHCCTTTEEEEEEHHHHHCHHHHHHHHHHHCCCEEEEECCCHHHHHTTTTCCCCHHHHHHHHHHHHCCEEEEECTTTTCCCCCTTTTHHHHHHHHCEEEECCCEEEEETTTCCCEEEECCCCCCCHHHHHHHHHHCCCEEEEECCCTTTTCCHHHHHHHHHHHHHHHHHHCCHHHHHHHCHHHHHHHHHHCHHHHHHHHCHHHHHHC... [Secondary structure assigned by YASARA]
1RSC-G  : ....LTYYTPDYTP.....KDTDLLAAFRFSPQPGVPADEAGAAIAAESST..............RYKGKCYHIE.............FAFIAYPLDLFEE.......SVTNILTSIVGNVFGFKAIRSLRLEDIRFPVALVKTFQGPPHGIQVERDLLNKY....RPMLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKSQAETGEIKGHYLNVTAPTCEEMMKRAEFAKEL..........IIMHDFLTAGFTANTTLAKWCRGVLLHIHRAMHAVIDR...NHGIHFRVLAKCLRLSGGDHLH...............LGFVDLMREDHIEA.FFTQDWASMPGVLPVASGGIHVWHMPALVEIF.GDDSVLQFGGGTLGHPWGNAPGATANRVALEACVQ...LREAGKWSPELAAALDLW................... [: RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (LARGE]
1GEH-B  : ..........GYEP.......RDIIAVFRVTPAEGYTIEQAAGAVAAESST..............DLSAKAYDFH.............IVRIAYPFHAFEE.......NLPGLLASIAGNIFGMKRVKGLRLEDLYFPEKLIREFDGPAFGIEGVRKMLEIK....RPIYGVVPKPKVGYSPEEFEKLAYDLLSNADYMKDDENLTSPWYNRFEERAEIMAKIIDKVENETGEKKTWFANITAD.LLEMEQRLEVLADL..........HAMVDVVITGWGALRYIRDLAAGLAIHGHRAMHAAFTR...YHGISMFVLAKLYRLIGIDQLH...............IQNARILRESHYK...LEQKFYSIKAAFPTSSGGLHPGNIQPVIEAL.GTDIVLQLGGGTLGHPDGPAAGARAVRQAIDAIMQGIPLDEYAKTHKELARALEKW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE]
1SVD-A  : .....TYWMPEYTP.....LDSDILACFKITPQPGVDREEAAAAVAAESSTG.............YYKGRAYRIE.............YAFIAYPIDLFEE.......SVVNVFTSLVGNVFGFKAVRGLRLEDVRFPLAYVKTCGGPPHGIQVERDKMNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFMRWRDRFLFVQDATETAEAQTGERKGHYLNVTAPTPEEMYKRAEFAKEI..........IIMHDYITGGFTANTGLAKWCQGVLLHIHRAMHAVIDR...NHGIHFRVLTKILRLSGGDHLH...............LGWIDLLRESFIP..FFDQDWGSMPGVFAVASGGIHVWHMPALVNIF.GDDSVLQFGGGTLGHPWGNAAGAAANRVALEACVE...LTAAAQHSPELKIAMETW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE]
2YBV-A  : ......YYTPDYTP.....KDTDILAAFRVTPQPGVPFEEAAAAVAAESSTG.............RYKGCCYDIE.............IAYIAYPLDLFEE.......SVTNMLTSIVGNVFGFKALKALRLEDLRIPVAYLKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKAQAETGEIKGHYLNVTAPTCEEMLKRAEFAKEL..........IIMHDFLTAGFTANTTLSKWCRGMLLHIHRAMHAVMDR...NHGIHFRVLAKCLRMSGGDHIH...............LGFVDLLRENYIE..YFTQDWASMPGVMAVASGGIHVWHMPALVDIF.GDDAVLQFG.....HPWGNAPGATANRVALEACIQ...IREAARWSPELAAAC...................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN]
1BXN-C  : ....MGYWDGDYVP.....KDTDLLALFRITPQDGVDPVEAAAAVAGESST..............MYRAKAYRVD.............FCYVAYDLSLFEE.......SIANLTASIIGNVFSFKPIKAARLEDMRFPVAYVKTFAGPSTGIIVERERLDKF....RPLLGATTKPKLGLSGRNYGRVVYEGLKGLDFMKDDENINSQPFMHWRDRFLFVMDAVNKASAATGEVKGSYLNVTAGTMEEMYRRAEFAKSL..........IIMVD.LIVGWTCIQSMSNWCRDMILHLHRAGHGTYTR...NHGVSFRVIAKWLRLAGVDHMH...............QGYYNVCRDAYTQ..FFDQDWASLRKVMPVASGGIHAGQMHQLIHLF.GDDVVLQFGGGTIGHPQGIQAGATANRVALEAMVL...LRDAARWCGPLRAALDTW................... [: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)]
1EJ7-L  : .....TYYTPEYQT.....KDTDILAAFRVTPQPGVPPEEAGAAVAAESSTG.............RYKGRCYRIE.............IAYVAYPLDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENVNSQPFMRWRDRFLFCAEALYKAQAETGEIKGHYLNATAGTCEEMIKRAVFAREL..........IVMHDYLTGGFTANTSLAHYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHIH...............LGFVDLLRDDFVE..YFTQDWVSLPGVLPVASGGIHVWHMPALTEIF.GDDSVLQFGGGTLGHPWGNAPGAVANRVALEACVK...IREACKWSPELAAACEVW................... [: RUBISCO (LARGE SUBUNIT)]
1IWA-C  : ....MGYWNPDYQV.....KDTDVLALFRVTPQPGVDPIEAAAAVAGESST..............LYRAKAYKVD.............FAYIAYELDLFEE.......SIANLTASIIGNVFGFKAVKALRLEDMRLPLAYLKTFQGPATGVILERERLDKF....RPLLGCTTKPKLGLSGKNYGRVVYEALKGLDFVKDDENINSQPFMRWRERYLFTMEAVNKASAATGEVKGHYLNVTAATMEEMYARANFAKEL..........IIMID.LVIGYTAIQTMAKWARDMILHLHRAGNSTYSR...NHGMNFRVICKWMRMAGVDHIH...............RGFYKTLLLPKLE..FFDMEWASLRKVMPVASGGIHAGQMHQLIHYLG.EDVVLQFGGGTIGHPDGIQAGATANRVALEAMIL...LREAAKTCGALRTALDLW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE]
1TEL-B  : .....GFFAS...........QYLVLDYYLESV..GDIETALAHFCSEQSTA.............VHAAKVIDYE.............RVTIAHPHCNFGP.......KIPNLLTAVCGETYFTPGVPVVKLMDIHFPDTYLADFEGPKFGIEGLRDILNAH....RPIFFGVVKPNIGLSPGEFAEIAYQSWLGLDIAKDDEMLADVTWSSIEERAAHLGKARRKAEAETGEPKIYLANITDE.VDSLMEKHDVAVRN..........ALLINALPVGLSAVRMLSNYT.QVPLIGHFPFIASFSR...KYGIHSKVMTKLQRLAGLDAVI...............LENVIECTKP..........MGRIKPCLPVPGGSDSALTLQTVYEKVGNVDFGFVPGRGVFGHPMGPKAGAKSIRQAWEAIEQGISIETWAETHPELQAMVDQ.................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE, LARGE SUBUNIT]
2D69-A  : .....DFVDLNYEP.....GRDELIVEYYFEPN.GVSPEEAAGRIASESSIG.............RSMAKVFYLE.............IAKIAYPLTLFEE.......SLVQLFSAVAGNVFGMKALKNLRLLDFHPPYEYLRHFKGPQFGVQGIREFMGVK....RPLTATVPKPKMGWSVEEYAEIAYELWSGIDLLKDDENFTSFPFNRFEERVRKLYRVRDRVEAETGETKEYLINITGP.VNIMEKRAEMVANE..........YVMIDIVVAGWSALQYMREVTEGLAIHAHRAMHAAFTR...RHGITMLALAKAARMIGVDQIH...............KRINDFLLS...........WEHIRPVFPVASGGLHPGLMPELIRLF.GKDLVIQAGGGVMGHPDGPRAGAKALRDAIDAAIEGVDLDEKAKSSPELKKSLREV................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE]
2QYG-D  : .....GFYAK...........NYIELDFDFECA..GDPHEAAAHLCSEQSTA.............RFAAKVLELS.............RVTIAHPHGNF........AKIPNLLSAVCGEVFFSPGIPLIRLQDIRFPEPYLAAFDGPRFGIAGVRERLQAF....RPIFFGVIKPNIGLPPQPFAELGYQSWTGLDIAKDDEMLADVDWCPLAERAALLGDACRRASAETGVPKIYLANITDE.VDRLTELHDVAVAN..........ALLINAMPVGLSAVRMLRKHA.TVPLIAHFPFIAAFSR...NYGIHSRVMTRLQRLAGFDVVI...............LDCIRACLE...........MGPIKPCLPVPGGSDSAATLENVYRKVGSADFGFVPGRGVFGHPMGPAAGATSIRQAWDAIAAGIPVPDHAASHPELAAALRAF................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE-LIKE PROTEIN 2]
2V67-A  : ....LTYYTPDYVV......DTDILAAFRMTPQPGVPPEECGAAVAAESST..............RYKGRCYDIE.............IAYVAYXIDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFVGXPHGIQVERDKLNKY....RGLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTXDDENVNSQPFMRWRDRFLFVAEAIYKAQAETGEVKGHYLNATAGTCEEMMKRAVXAKEL..........IIMHDYLTGGFTANTSLAIYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHLH...............LGFVDLMRDDYVE..YFTQDWXSMPGVMPVASGGIHVWHMPALVEIF.GDDACLQFGGGTLGHPWGNAPGAAANRVALEACTQ...IRSACKWSPELAAACEVW................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN]
3NWR-A  : ....................EDTLEADYLIET..PLDPARVADVMAGEQSSG.............RSRASVLRIE.............RITLSFPLANI.........NLPTLAATVAGNLYDLGEVTGVRLLSLRLPASYRARFELPRHGVAGTRALTDVK....RPMIGTIIKPNVGLSAAETAALVRELCEAVDFIXDDEVCANPAHAPLAERVRAVMSEVRRYRERSGRPVMVAFNITDD.LDAMRRHAELVERE..........CVMASINWCGFSAIQSLRRTT.PLVLHAHRNGYGMMSR...ALGMSFQAYQTLWRLSGVDHMH...............IESARDCATP...............AVLPAFSSGQWAGTVQATFDAVRSTDLLFMSGGGILAHPDGPAAGVTSVRQAWAAVQAGTPLPVYAEHMPELRRALAFF................... [: A RUBISCO-LIKE PROTEIN]
3QFW-B  : ......................RIVATYHIAS.....IEQRALALAIEQSVE.............NIVGRVEDVA.............AVRIGLAAATAP.......AEPGQLLNMLFGNSSIQPD...IALADVELPAHYLTAFGGPRVGLAGIRTLTGAQ....RALTASALKP.QGLSPAALASIAHQLALGVDLIKDDHGLADQAFSPFAERAAAVGKAVREANAARGGRTLYAPNISG.TLDDMRRQLGVIRDE..........AVLVAPMIVGVSNFHAIVKEAAGLVVVAHPAMAGAA........IAAPLLGRLFRLFGADATV...............LALAQAARD...........FGKLNACIPTPAGGIMLQRVNELLRFYG.QDVMLLI..........LTEQASRFVNKVADYGQR....................................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE]
uniref90: ......................RFTATYRIAA.....AKKIARGIAVEQTVE.............SVIGQIEDLK.............YAIISYSPDTVE.......GEMTELMNMLFGNTSLQPG...IRLMSFELPDSMYRHYPGPKFGRQGIRELCGIE....GPILMSALKP.LGRSAKDFGETAYKLALGCPLIKDDHSLFNQSYAPFKDRVKACVDSVNNANAKTGGRSLYIANCTA.DSMEFLERAMTAQEL..........GIMAAPGLLGLSIIRELSSAPFHLPIFLHPCFSGPL........LSADCCGQFSRLAGADAAI...............RKICDGTET...........MGGLRSIFPVPSGGMKWQLFKKMVQVYG.PDAIFLV................................................................... [uniref90|C9LQN5 Putative 2,3-diketo-5-methylthiopentyl-1-phosphate enolase n=1 Tax=Dialister invisus DSM 15470 RepID=C9LQN5_9FIRM]
2ZVI-A  : ......................ELLATYLLT.....DTEKKAEQIATGLTVG.............KHKGRVIKVE.............VITIAYPEINFSQ.......DIPALLTTVFGKLSL...DGKIKLIDLHFSEAFKRALPGPKFGVYGIRKLLGE.....RPLLMSIFKGVIGRDLSDIKEQLRQQALGVDLIKDDEIFFETGLAPFETRIAEGKQILKETYEQTGHKTLYAVNLTGR.TADLKDKARRAAEL..........ALLFNVFAYGLDVMQGLAED..PVPIMAHPAVSGAFTS...FYGFSHALLGKLNRYCGADFSL...............LAIHEECVR.............AFNQTFAVPSAGIHPGMVPLLMRDF.GIDHIINAGGGVHGHPNGAQGGGRAFRAIIDAVLEAQPIDEKAEQCKDLKLALDKWGK................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE]
uniref90: ....................................DAVKQAKIIAVGQTAG.............SHLAEVINI..............IATVSFPETNVEN.......DIPSLLTMIFGKYSM...AGTAKVVAVRLPASYGMR...PKLGIAGIRDRLGV.....RPLVMAIFKPALGLTASDHAEILSEVAFALDIIKDDEILGDLASAPTLERLRACREVIARVKQETGRTVLYAVNVTGN.ATKIVERARMLVKE..........ALLLNVLAYGFAVLEAIASD..NVPIFAHPALAGALCI...DCGMAYSVVGTLMAHGGADAVL...............GKIRDILRD.............VF....PVPSAGIHPGIIPNIIADY.GQDVILNSGTGIMDHADGPAAGVKAFFDALDRVKKGEIFNQPGD............................... [uniref90|D8FUJ2 2,3-diketo-5-methylthiopentyl-1-phosphate enolase n=1 Tax=Oscillatoria sp. PCC 6506 RepID=D8FUJ2_9CYAN]
2OEK-B  : ......................AVMATYLLHDE..TDIRKKAEGIALGLTIG.............KHKGEVVAIE.............IVKIAYPTVNFSA.......DLPALLVTTFGKLSLD...GEVRLLDLEFPDEWKRQFPGPRFGIDGIRDRVGVH....RPLLMSIFKGMIGRDLAYLTSELKKQALGVDLVXDDEILFDSELLPFEKRITEGKAALQEVYEQTGKRTLYAVNLTGK.TFALKDKAKRAAEL..........VLLFNVFAYGLDVLQALRED..AVPIMAHPAFSGAVTP...FYGVAPSLWGKLLRLAGADFVL...............LGIARALTD.............PFARAFPVPSAGIHPGLVPLIIRDF.GLDTIVNAGGGIHGHPDGAIGGGRAFRAAIDAVLAGRPLRAAAAENEALQKAIDRWGV................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE ENOLASE]
uniref90: ........................IATYRSHDD..ADFHKKAQGIAVGLTVG.............KHLGKVLSVD.............DIRIAYPDVNFSR.......DIPALLVTIFGKLSMD...GRIKLIDLDVSNEFRSAFPGPKFGLEGVRKLVGVQ....RPLLMSIFKSVIGHDLSGLEEQFYRQALGVDLIKDDEILFENPLTPLEKRVETCMRAARKAKEATGQELLYAVNLTGP.TSQLNANARKAIQA..........ALLFNVLAYGYDALHELSAD..NVPIAAHPSLAGAFYP...HYGIAAPVLGKLMRLAGADLTL...............MAVRDALLD.............SLRKSFPVPSAGIHPGLVPLILRDF.GNDVVVNAGGGVHGHPLGTEAGGQAFRQAIDATLAGQKLAEAAAGHEALQAAITAWGV................. [uniref90|E0IC30 2,3-diketo-5-methylthiopentyl-1-phosphate enolase n=1 Tax=Paenibacillus curdlanolyticus YK9 RepID=E0IC30_9BACL]
3FK4-A  : ......................GIIATYLIHDD...NLEKKAEQIALGLTIG.............QHKGNVIHVE.............IIKIEYPLLNFSP.......DLPAILTTTFGKLSLD...GEVKLIDLTFSDELKKHFPGPKFGIDGIRNLLQVH....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENALTPLTKRIVSGKEVLQSVYETYGHKTLYAVNLTGR.TFDLKENAKRAVQA..........ILLFNVFAYGLDVLQSLAED..PVPIMAHPAVSGAYSA...LYGVSSPLLGKLLRYAGADFSL...............LAISKYLTE...........DASFKKSFSVPSAGIHPGFVPFIVRDF.GKDVVINAGGGIHGHPNGAQGGGKAFRTAIDATLQNKPLHEV..DDINLHSALQIWG.................. [: RUBISCO-LIKE PROTEIN]
uniref90: ......................GIIATYVIHDD...NLTKKAEQIALGLTIG.............QHKGNVVHVE.............IIKIQYPSLNFSP.......DLPAILTTAFGKLSLD...GEIKLIDLTFSDDLKRQFSGPKFGIEEVRKRLHVH....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENALTPLEKRVRSGKEVLQSVYETYGHRTLYAVNITGR.TYDVKENAKRAVNA..........LLLFNAFAYGLDVLQLLAED..NVPIMAHPAISGAYTS...LYGFSHSLLGKLLRYAGADFSL...............LQIAETLTI...........DSHLKRSFPVPSAGIHPGFVPFILRDF.GNDVVINAGGGIHGHPNGAQGGGKAFRAAIDATLQGTPLHEV..DDADLHTALQLWG.................. [uniref90|A7GS60 2,3-diketo-5-methylthiopentyl-1-phosphate enolase n=1 Tax=Bacillus cytotoxicus NVH 391-98 RepID=MTNW_BACCN]

NOTE: To save space, only 20 of 1113 template profile alignments are shown above. The complete set of alignments can be found in the file Homology_7t1c-~_profile.ali. The template profile contains structural alignments of 16 PDB files, which provide safe anchors for the remaining sequence-based alignments (only reliable regions shown).

In the alignment above, 450 of 470 target residues (95.7%) are aligned to template residues. Among these aligned residues, the sequence identity is 81.3% and the sequence similarity is 88.4% ('similar' means that the BLOSUM62 score is > 0). The following 4 loops had to be modeled (only the first of 2 similar loops in the homodimer is listed):

LoopN-terminal anchorLoop sequenceC-terminal anchor
1TAFGDDPVKGGGLFK
3SSTGTNVEVSTTDDFTRGVDAL
5NoneMDQSNR
7REKLGVHKNone

After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).

The resulting half-refined model has been saved as Homology_7t1c-~01_refined050.yob and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals0.571Optimal
Packing 1D-0.358Good
Packing 3D-0.851Good
Overall-0.453Good

Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as Homology_7t1c-~01_refined100.yob, the corresponding Z-scores are listed below:

Check typeQuality Z-scoreComment
Dihedrals0.777Optimal
Packing 1D-0.055Good
Packing 3D-1.013Satisfactory
Overall-0.380Good

Since the overall quality Z-score improved to -0.380 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.

NOTE: 8 residues contained in N- and C-terminal unaligned tails of the homodimeric model have been excluded from the Z-scores in both tables above, since they are not reliable (YASARA does not yet perform ab initio structure prediction) and would have mainly added noise to the result.

The final model for this template and alignment has been saved as Homology_7t1c-~01.yob, and is shown below, together with a plot of its overall quality Z-score, shown per residue:

6.2. Homology model 2/15, based on template 7T1C-~, alignment variant 02

This model is a homodimer, and based on the following profile-profile alignment:

(To improve readability, only up to ten lines of the complete target multiple sequence alignment (MSA) shown above are also displayed here (upside down). The template MSA has been shrunk and focused on structurally aligned PDB entries. The actual target-template alignment can be found in the middle at the line named 'Match'.)

Q08EW6  : .......................................................................................................................NNQGGGDIEHAKIHGIYMPERAIQLFDGPSKDISDMWRILGRPVKDGGYNAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEIQGNQVFSPMNQTIPLVVDAMKRAQDETGQAKLFSANITADDQYEMCARADFILEAFGP..DADKVAFLVDGYVGDPGMITTARSQYPNQYLHYHRAGHGAVNSPKIKRGYTAFVLAKMSRLQGASGAHVGTMGYGKME................................................................................................................................ [uniref90|Q08EW6 Ribulose 1,5-bisphosphate carboxylase/oxygenase large subunit (Fragment) n=1 Tax=uncultured marine bacterium RepID=Q08EW6_9BACT]
Q5DVV5  : ............................................................................................................................................................................IIKPKLGLRPKPFAEACYNFWLGGDFIKNDEPQGNQIWGPIKEVVPLVKDSLVRAQDDTGMAKLFSFNITADDHYEMLHRGEYILETFAEFSE..NIAFLVDGCVGGPGMVTTARRNFPDQFLHYHRAGHGAVTSDQSDRGYNMLVHMKMARLQGASGIHTGTMGYGKMEGAADDKVIAYMLERDSADGLSYHQEWEGMKATTPIICGGMNA...................................................................................... [uniref90|Q5DVV5 Ribulose-1,5-bisphosphate carboxylase oxygenase large subunit (Fragment) n=11 Tax=uncultured prokaryote RepID=Q5DVV5_9ZZZZ]
Q933G7  : ........................................................................................................................................VPPAYLRLFDGPSTTIKDLWRVLGRPVVDGGFIVGTIIKPKLGLRPQPFADACYDFWLGGDFIKNDEPQGNQVFAPFKDTVRAVNDAMRRAQDATGQPKLFSFNITADDHYEMLARGEYILETFGE..NADHVAFLVDGYVAGPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHVGTMGYGKMEGEASDRDSAFMITQDSAEGPYFKQEW...................................................................................................... [uniref90|Q933G7 Form II ribulose 1,5-bisphosphate carboxylase/oxygenase (Fragment) n=5 Tax=Rhodopseudomonas palustris RepID=Q933G7_RHOPA]
F2ZCE9  : .....................................................................................................................................DFYVPPDFLRLFDGPATTISNLWRVLGRPHQNGGFIVGTIVKPKLGLRPRPFADACYDFWLGGDFIKNDEPQGNQTFSPLKETIPLVADAMRRAQDETGEAKLFSANITADDHYEMVARGEFILDTFGEF..ADHVAFLVDGYVAGAAAVTTARRSFPQQYLHYHRAGHGAITSPQSKRGYTAFVHCKMARLQGASGIHTGTMSFGKMEGEAADRAIAFMLEQDSADGPYFHQEWHGMNPTTSIISG.......................................................................................... [uniref90|F2ZCE9 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=1 Tax=uncultured bacterium RepID=F2ZCE9_9BACT]
F2ZCD0  : ......................................................................................................................GNNQGMGDIANAQMQDFYVPPAMLALFDGPAKSINDLWTLLGRDNENGGYIAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEPQGNQVFCPLKKVLPLVHDAMKRAQDETGEAKLFSLNITADDHYEMCARADFGLETFGE..DAPRLAFLVDGFVGGPGMVTTARRQYSSQYLHYHRAGHGMITSPSSKRGYTAYILAKMSRLMGASGIHVGTMGYGKMEGGADDKIIAYMIERDECQGPFYYQKWHGMKPTTPIVSGGM........................................................................................ [uniref90|F2ZCD0 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=4 Tax=uncultured bacterium RepID=F2ZCD0_9BACT]
F5BZE6  : ......................................................................................................................GNNQGMGDVEYAKMIDFYMARSLLTLFDGPAMNITDMWRVLGRPQVNGGMVVGTIIKPKLGLRPKPFADACYMFWMGGDFIKNDEPQGNQVFAPTREIIPLVAEAMERAQQETGEAKIFSANITADDPFEMIRRGEFILEAFGK..NASHVAFLVDGYVGGPSAVTLCRRYFPNQFLHYHRAGHGAVTSNQSKRGYTVLTHMKMSRLQGASGIHTGTMGYGKMEGDKNEKMVAYMIERDEAMGVYYNQPWHGMTATTPIISGGMNALR.................................................................................... [uniref90|F5BZE6 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II (Fragment) n=1 Tax=alpha proteobacterium LM-5 RepID=F5BZE6_9PROT]
Q9FPW1  : LDQSSRYADLSLDEATLVKNGKHVLVAYIMKPKAGYDYLATAAHFAAESSTGTNVNVCTTDDFTKSVDALVYYIDPDSEE.........MKIAYPTLLFDRNIIDGRGMMCSFLTLAIGNNQGMGDVEYGKIYDFYLPPSFLRLYDGPAVNVEDMWRILGKGTSNGGLVDGTIIKPKLGLQPNPFGEACYSFWQGGDFIKNDEPQGNQVFCQMNECIPEVVKAMRACVKETGSSKLFSANITADDPEEMIARGKYIMSQFGPLSE..NCAFLVDGYVAGGTAVTCCRRNFPKQFLHYHRAGHGSVTSPQTQRGYTAFVHTKISRVIGASGIHVGTMSFGKMEGDASDKNIAYMLQDDEADGPYYRQEWQGMKETTPIISGGMNALRLPAFFENLGHSNVILTAGGGSFGHKDGPKIGAISCRQGEEAWKSLSDVIEYAKTHEEIKGAFLTFQKDADQIYPGWKEKLG... [uniref90|Q9FPW1 Ribulose 1,5-bisphosphate carboxylase oxygenase large subunit n=1 Tax=Symbiodinium sp. RepID=Q9FPW1_SYMSP]
E6VVI6  : .DQTSRYVNFDLKEDQLIADGNHVLCAYIYKPANGYGNVEVAAHFAAESSTGTNVEVCTTDDFTKGVDALVYEVSDASNGDS......LMKIAYPVELFDRNIIDGRAMLASFLTLCIGNNQGMGDVAYAKMHDFYVPRQYLELFDGPSKNIADFWRMLGRPTENGGMIAGTIVKPKLGLRPKPFADACYHFWLGGDFVKNDEPQGNQVFAPLKETITAVADAMRRAQDETGEAKIFSANITADDPREMIARGEFILNAFGE..NASRVAFLVDGYVAGPTAITTARRNFPNQFLHYHRAGHGAVTSPQAKRGYTAFVLSKMSRLQGASGIHTGTMGFGKMEGEMADKSMAYMIEREEAQGPYFKQKWYGMKATTPMISGGMNALRLPGFFDNLGHSNICQTSGGGAFGHLDGPTAGALSLRQSHDAWIQGVNLLDYAKEHNELARAFESFPGDADRFYPTWRHQL.... [uniref90|E6VVI6 Ribulose-bisphosphate carboxylase n=1 Tax=Desulfovibrio aespoeensis Aspo-2 RepID=E6VVI6_DESAO]
Q8RTI1  : MDQSNRYADLSLKEDDLIKGGNHVLVAYLMKPKTGYGYLEAAAHFSAESSTGTNVEVSTTDDFTKGVDALVYEIDEAK.........EIMKIAYPVDLFDRNITDGRAMIVSFLTLAIGNNQGMGDIAYAKMLDFYVPQKYLRLFDGPSKDISDLWRILGRPVVNGGYIAGTIIKPKLGLRPKPFAEAAYQFWLGGDFIKNDEPQGNQVFSPMRETIPLVYDSMKRAMDETGEAKLFSANITADDHYEMMARGEFILNTFGP..DADKVAFLVDGYVGGPGMVTTARRHFANQYLHYHRAGHGAVTSPSAKRGYTAFVLAKMSRLQGASGIHVGTMGYGKMEGDATDKNIAYMIERDSADGPFYHQEWYGMKPTTPIISGGMNALRLPGFFENLGHANLINTSGGGSYGHIDSPAAGAISLRQAYECWQQGADPIEFAKEHKEFARAFESFPGDADTIFPGWREKLGVHK [uniref90|Q8RTI1 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II n=1 Tax=magnetite-containing magnetic vibrio RepID=Q8RTI1_9PROT]
Q0F2Z8  : MDQSNRYADLSLNEADLIAGGKHLLVAYKLIPAKGYGFLEVAAHIAAESSTGTNVEVSTTDDFTRGVDALVYDIDETAFGDEGVTGGGLMKVAYPVELFDPNLIDGHYNVSHMWSLILGNNQGMGDHEGLRMLDFMVPECMIRKFDGPSAGIADLWKVLGRPEVDGGYISGTIIKPKLGLRPEPFAKACLDFWLGGDFIKNDEPQANQPFCPMKVVIPKVAEAMDRAQQETGQAKLFSANATADYHGECVARGEYILSEFAKYGNEKHVAFLIDGFVTGPAGVTTARRAFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLARLQGASGIHTGTMGYGKMEGHGKETVLAYMLERDECMGHYFNQKWYGMKPTAPIISGGMNALRLPGFFENLGHGNVINTCGGGSFGHIDSPAAGGKSLDQAYDCWKSGTDPIEYAKTHGEFARAFESFPGDADKLYPGWRDKLGVHK [uniref90|Q0F2Z8 Ribulose-bisphosphate carboxylase n=1 Tax=Mariprofundus ferrooxydans PV-1 RepID=Q0F2Z8_9PROT]
SecStr  : CCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCEEECCCCCCHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCEEEECCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEECCCCCCHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCHHCCCCCCCEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHHHHCCCC [Secondary structure predicted by PsiPred]
Target  : MDQSNRYANLNLKEEDLIKNGKHLLVAYKLIPAKGHGFLEVAAHVAAESSTGTNVEVSTTDDFTRGVDALVYEIDETAFGDDPVKGGGLFKVAYPVELFDPNLTDGTYNISHMWSLILGNNQGMGDHQGLRMLDFLVPEMMVRKFDGPSANISNLWKVLGRSETDGGYIAGTIIKPKLGLRPEPFAKACYDFWLGGDFIKNDEPQANQPFCPMEVVMPKVAEAMDRAQQATGQAKLFSANITADYYKEMIHRGDFVLETFAKYNSASHVAFLVDGFVTGPAGVTTARREFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLVRLMGASGMHTGTMGYGKMEGHGKETVLAYMLERDECQGPYFYQKWYGMKATTPIISGGMNALRLPGFFQNLGHGNVINTCGGGAFGHIDSPAAGGISLGQAYDCWKSGSDPIEYAKTHKEFARAFESFPKDGDKLFAGWREKLGVHK
Match   :  DQSNRYANL:LKEEDLI::G|H|LVAY|| PA G|GFLEVAAH|AAESSTGT           RGVDALVYEIDETAFGD:   GG L:K|AYPVELFD NL D  | |SHMWSL|LGNNQGMGDH GLRMLDF :PE:MVR:FDGP::NI::|W|VLGR   DGGYIAGTIIKPKLGLRPEPFAKACYDFWLGG FIKNDEPQANQ F:PM: V:P VAEAMDRAQQ TG|AKLFSANITAD|| EMI RG|||L: FAKY:: :HVAFLVDGFVTGPAGV:TAR: FP TFLHFHRAGHGA:TSYKSPMGMDPLCYMKL:RL:GASG:HTGTMGYGKMEGH: E VLAYMLERDECQGPYFYQKWYGMKATTPIISGGMNALRL GFF|NLGH:NVINTCGGG:FGHID:PAAGG SL QAY:CWK:G:DPIE|AK HKEFARAFESFP D:DKLF GWREKLG   
Template: .DQSNRYANLDLKEEDLINGGRHMLVAYRMKPAPGYGFLEVAAHIAAESSTGT...........RGVDALVYEIDETAFGDQ...GG.LLKIAYPVELFDHNLIDDKHPVSHMWSLVLGNNQGMGDHLGLRMLDFYLPEVMVRNFDGPATNIEDMWRVLGRPTKDGGYIAGTIIKPKLGLRPEPFAKACYDFWLGGTFIKNDEPQANQTFAPMKKVIPLVAEAMDRAQQETGEAKLFSANITADFFGEMIARGEYILNEFAKYGNEDHVAFLVDGFVTGPAGVATARHYFPKTFLHFHRAGHGALTSYKSPMGMDPLCYMKLARLQGASGIHTGTMGYGKMEGHSDERVLAYMLERDECQGPYFYQKWYGMKATTPIISGGMNALRLIGFFENLGHANVINTCGGGSFGHIDGPAAGGKSLDQAYQCWKEGADPIEFAKEHKEFARAFESFPWDADKLFPGWREKLG...
SecStr  : .CHHHHHCTTTTHHHHHHHHCCCEEEEEEEECTTTTHHHHHHHHHHHHHCCCC...........GGCCCEEEEEETTTTTTT...CE.EEEEEETTTTCCCCCCCCCCHHHHHHHHHHGGGGCCCCCEEEEEEEEECHHHHHHCCCCCCCCHHHHHHHHCCCCCCCCCEEEECCCCCCCCHHHHHHHHHHHHHHCCEEEEETTTTCCTTTTHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCHHHHHHHHHHHHHHHHHHCCTTTEEEEEEHHHHHCHHHHHHHHHHHCCCEEEEECCCHHHHHTTTTCCCCHHHHHHHHHHHHCCEEEEECTTTTCCCCCTTTTHHHHHHHHCEEEECCCEEEEETTTCCCEEEECCCCCCCHHHHHHHHHHCCCEEEEECCCTTTTCCHHHHHHHHHHHHHHHHHHCCHHHHHHHCHHHHHHHHHHCHHHHHHHHCHHHHHHC... [Secondary structure assigned by YASARA]
1RSC-G  : ....LTYYTPDYTP.....KDTDLLAAFRFSPQPGVPADEAGAAIAAESST.............DRYKGKCYHIE.............FAFIAYPLDLFEE.......SVTNILTSIVGNVFGFKAIRSLRLEDIRFPVALVKTFQGPPHGIQVERDLLNKY....RPMLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKSQAETGEIKGHYLNVTAPTCEEMMKRAEFAKEL..........IIMHDFLTAGFTANTTLAKWCRGVLLHIHRAMHAVIDR...NHGIHFRVLAKCLRLSGGDHLH...............LGFVDLMREDHIEA.FFTQDWASMPGVLPVASGGIHVWHMPALVEIF.GDDSVLQFGGGTLGHPWGNAPGATANRVALEACVQ...LREAGKWSPELAAALDLW................... [: RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (LARGE]
1GEH-B  : ..........GYEP.......RDIIAVFRVTPAEGYTIEQAAGAVAAESST.............ADLSAKAYDFH.............IVRIAYPFHAFEE.......NLPGLLASIAGNIFGMKRVKGLRLEDLYFPEKLIREFDGPAFGIEGVRKMLEIK....RPIYGVVPKPKVGYSPEEFEKLAYDLLSNADYMKDDENLTSPWYNRFEERAEIMAKIIDKVENETGEKKTWFANITAD.LLEMEQRLEVLADL..........HAMVDVVITGWGALRYIRDLAAGLAIHGHRAMHAAFTR...YHGISMFVLAKLYRLIGIDQLH...............IQNARILRESHYK...LEQKFYSIKAAFPTSSGGLHPGNIQPVIEAL.GTDIVLQLGGGTLGHPDGPAAGARAVRQAIDAIMQGIPLDEYAKTHKELARALEKW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE]
1SVD-A  : .....TYWMPEYTP.....LDSDILACFKITPQPGVDREEAAAAVAAESSTG............DYYKGRAYRIE.............YAFIAYPIDLFEE.......SVVNVFTSLVGNVFGFKAVRGLRLEDVRFPLAYVKTCGGPPHGIQVERDKMNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFMRWRDRFLFVQDATETAEAQTGERKGHYLNVTAPTPEEMYKRAEFAKEI..........IIMHDYITGGFTANTGLAKWCQGVLLHIHRAMHAVIDR...NHGIHFRVLTKILRLSGGDHLH...............LGWIDLLRESFIP..FFDQDWGSMPGVFAVASGGIHVWHMPALVNIF.GDDSVLQFGGGTLGHPWGNAAGAAANRVALEACVE...LTAAAQHSPELKIAMETW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE]
2YBV-A  : ......YYTPDYTP.....KDTDILAAFRVTPQPGVPFEEAAAAVAAESSTG............DRYKGCCYDIE.............IAYIAYPLDLFEE.......SVTNMLTSIVGNVFGFKALKALRLEDLRIPVAYLKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKAQAETGEIKGHYLNVTAPTCEEMLKRAEFAKEL..........IIMHDFLTAGFTANTTLSKWCRGMLLHIHRAMHAVMDR...NHGIHFRVLAKCLRMSGGDHIH...............LGFVDLLRENYIE..YFTQDWASMPGVMAVASGGIHVWHMPALVDIF.GDDAVLQFG.....HPWGNAPGATANRVALEACIQ...IREAARWSPELAAAC...................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN]
1BXN-C  : ....MGYWDGDYVP.....KDTDLLALFRITPQDGVDPVEAAAAVAGESST.............DMYRAKAYRVD.............FCYVAYDLSLFEE.......SIANLTASIIGNVFSFKPIKAARLEDMRFPVAYVKTFAGPSTGIIVERERLDKF....RPLLGATTKPKLGLSGRNYGRVVYEGLKGLDFMKDDENINSQPFMHWRDRFLFVMDAVNKASAATGEVKGSYLNVTAGTMEEMYRRAEFAKSL..........IIMVD.LIVGWTCIQSMSNWCRDMILHLHRAGHGTYTR...NHGVSFRVIAKWLRLAGVDHMH...............QGYYNVCRDAYTQ..FFDQDWASLRKVMPVASGGIHAGQMHQLIHLF.GDDVVLQFGGGTIGHPQGIQAGATANRVALEAMVL...LRDAARWCGPLRAALDTW................... [: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)]
1EJ7-L  : .....TYYTPEYQT.....KDTDILAAFRVTPQPGVPPEEAGAAVAAESSTG............DRYKGRCYRIE.............IAYVAYPLDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENVNSQPFMRWRDRFLFCAEALYKAQAETGEIKGHYLNATAGTCEEMIKRAVFAREL..........IVMHDYLTGGFTANTSLAHYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHIH...............LGFVDLLRDDFVE..YFTQDWVSLPGVLPVASGGIHVWHMPALTEIF.GDDSVLQFGGGTLGHPWGNAPGAVANRVALEACVK...IREACKWSPELAAACEVW................... [: RUBISCO (LARGE SUBUNIT)]
1IWA-C  : ....MGYWNPDYQV.....KDTDVLALFRVTPQPGVDPIEAAAAVAGESST.............DLYRAKAYKVD.............FAYIAYELDLFEE.......SIANLTASIIGNVFGFKAVKALRLEDMRLPLAYLKTFQGPATGVILERERLDKF....RPLLGCTTKPKLGLSGKNYGRVVYEALKGLDFVKDDENINSQPFMRWRERYLFTMEAVNKASAATGEVKGHYLNVTAATMEEMYARANFAKEL..........IIMID.LVIGYTAIQTMAKWARDMILHLHRAGNSTYSR...NHGMNFRVICKWMRMAGVDHIH...............RGFYKTLLLPKLE..FFDMEWASLRKVMPVASGGIHAGQMHQLIHYLG.EDVVLQFGGGTIGHPDGIQAGATANRVALEAMIL...LREAAKTCGALRTALDLW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE]
1TEL-B  : .....GFFAS...........QYLVLDYYLESV..GDIETALAHFCSEQSTA............RVHAAKVIDYE.............RVTIAHPHCNFGP.......KIPNLLTAVCGETYFTPGVPVVKLMDIHFPDTYLADFEGPKFGIEGLRDILNAH....RPIFFGVVKPNIGLSPGEFAEIAYQSWLGLDIAKDDEMLADVTWSSIEERAAHLGKARRKAEAETGEPKIYLANITDE.VDSLMEKHDVAVRN..........ALLINALPVGLSAVRMLSNYT.QVPLIGHFPFIASFSR...KYGIHSKVMTKLQRLAGLDAVI...............LENVIECTKP..........MGRIKPCLPVPGGSDSALTLQTVYEKVGNVDFGFVPGRGVFGHPMGPKAGAKSIRQAWEAIEQGISIETWAETHPELQAMVDQ.................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE, LARGE SUBUNIT]
2D69-A  : .....DFVDLNYEP.....GRDELIVEYYFEPN.GVSPEEAAGRIASESSIG............KRSMAKVFYLE.............IAKIAYPLTLFEE.......SLVQLFSAVAGNVFGMKALKNLRLLDFHPPYEYLRHFKGPQFGVQGIREFMGVK....RPLTATVPKPKMGWSVEEYAEIAYELWSGIDLLKDDENFTSFPFNRFEERVRKLYRVRDRVEAETGETKEYLINITGP.VNIMEKRAEMVANE..........YVMIDIVVAGWSALQYMREVTEGLAIHAHRAMHAAFTR...RHGITMLALAKAARMIGVDQIH...............KRINDFLLS...........WEHIRPVFPVASGGLHPGLMPELIRLF.GKDLVIQAGGGVMGHPDGPRAGAKALRDAIDAAIEGVDLDEKAKSSPELKKSLREV................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE]
2QYG-D  : .....GFYAK...........NYIELDFDFECA..GDPHEAAAHLCSEQSTA............PRFAAKVLELS.............RVTIAHPHGNF........AKIPNLLSAVCGEVFFSPGIPLIRLQDIRFPEPYLAAFDGPRFGIAGVRERLQAF....RPIFFGVIKPNIGLPPQPFAELGYQSWTGLDIAKDDEMLADVDWCPLAERAALLGDACRRASAETGVPKIYLANITDE.VDRLTELHDVAVAN..........ALLINAMPVGLSAVRMLRKHA.TVPLIAHFPFIAAFSR...NYGIHSRVMTRLQRLAGFDVVI...............LDCIRACLE...........MGPIKPCLPVPGGSDSAATLENVYRKVGSADFGFVPGRGVFGHPMGPAAGATSIRQAWDAIAAGIPVPDHAASHPELAAALRAF................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE-LIKE PROTEIN 2]
2V67-A  : ....LTYYTPDYVV......DTDILAAFRMTPQPGVPPEECGAAVAAESST.............DRYKGRCYDIE.............IAYVAYXIDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFVGXPHGIQVERDKLNKY....RGLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTXDDENVNSQPFMRWRDRFLFVAEAIYKAQAETGEVKGHYLNATAGTCEEMMKRAVXAKEL..........IIMHDYLTGGFTANTSLAIYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHLH...............LGFVDLMRDDYVE..YFTQDWXSMPGVMPVASGGIHVWHMPALVEIF.GDDACLQFGGGTLGHPWGNAPGAAANRVALEACTQ...IRSACKWSPELAAACEVW................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN]
3NWR-A  : ....................EDTLEADYLIET..PLDPARVADVMAGEQSSG............ARSRASVLRIE.............RITLSFPLANI.........NLPTLAATVAGNLYDLGEVTGVRLLSLRLPASYRARFELPRHGVAGTRALTDVK....RPMIGTIIKPNVGLSAAETAALVRELCEAVDFIXDDEVCANPAHAPLAERVRAVMSEVRRYRERSGRPVMVAFNITDD.LDAMRRHAELVERE..........CVMASINWCGFSAIQSLRRTT.PLVLHAHRNGYGMMSR...ALGMSFQAYQTLWRLSGVDHMH...............IESARDCATP...............AVLPAFSSGQWAGTVQATFDAVRSTDLLFMSGGGILAHPDGPAAGVTSVRQAWAAVQAGTPLPVYAEHMPELRRALAFF................... [: A RUBISCO-LIKE PROTEIN]
3QFW-B  : ......................RIVATYHIAS.....IEQRALALAIEQSVE.............NIVGRVEDVA.............AVRIGLAAATAP.......AEPGQLLNMLFGNSSIQPD...IALADVELPAHYLTAFGGPRVGLAGIRTLTGAQ....RALTASALKP.QGLSPAALASIAHQLALGVDLIKDDHGLADQAFSPFAERAAAVGKAVREANAARGGRTLYAPNISG.TLDDMRRQLGVIRDE..........AVLVAPMIVGVSNFHAIVKEAAGLVVVAHPAMAGAA........IAAPLLGRLFRLFGADATV...............LALAQAARD...........FGKLNACIPTPAGGIMLQRVNELLRFYG.QDVMLLI..........LTEQASRFVNKVADYGQR....................................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE]
uniref90: ......................RFTATYRIAA.....AKKIARGIAVEQTVE.............SVIGQIEDLK.............YAIISYSPDTVE.......GEMTELMNMLFGNTSLQPG...IRLMSFELPDSMYRHYPGPKFGRQGIRELCGIE....GPILMSALKP.LGRSAKDFGETAYKLALGCPLIKDDHSLFNQSYAPFKDRVKACVDSVNNANAKTGGRSLYIANCTA.DSMEFLERAMTAQEL..........GIMAAPGLLGLSIIRELSSAPFHLPIFLHPCFSGPL........LSADCCGQFSRLAGADAAI...............RKICDGTET...........MGGLRSIFPVPSGGMKWQLFKKMVQVYG.PDAIFLV................................................................... [uniref90|C9LQN5 Putative 2,3-diketo-5-methylthiopentyl-1-phosphate enolase n=1 Tax=Dialister invisus DSM 15470 RepID=C9LQN5_9FIRM]
2ZVI-A  : ......................ELLATYLLT.....DTEKKAEQIATGLTVG............QKHKGRVIKVE.............VITIAYPEINFSQ.......DIPALLTTVFGKLSL...DGKIKLIDLHFSEAFKRALPGPKFGVYGIRKLLGE.....RPLLMSIFKGVIGRDLSDIKEQLRQQALGVDLIKDDEIFFETGLAPFETRIAEGKQILKETYEQTGHKTLYAVNLTGR.TADLKDKARRAAEL..........ALLFNVFAYGLDVMQGLAED..PVPIMAHPAVSGAFTS...FYGFSHALLGKLNRYCGADFSL...............LAIHEECVR.............AFNQTFAVPSAGIHPGMVPLLMRDF.GIDHIINAGGGVHGHPNGAQGGGRAFRAIIDAVLEAQPIDEKAEQCKDLKLALDKWGK................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE]
uniref90: ....................................DAVKQAKIIAVGQTAG............RSHLAEVINI..............IATVSFPETNVEN.......DIPSLLTMIFGKYSM...AGTAKVVAVRLPASYGMR...PKLGIAGIRDRLGV.....RPLVMAIFKPALGLTASDHAEILSEVAFALDIIKDDEILGDLASAPTLERLRACREVIARVKQETGRTVLYAVNVTGN.ATKIVERARMLVKE..........ALLLNVLAYGFAVLEAIASD..NVPIFAHPALAGALCI...DCGMAYSVVGTLMAHGGADAVL...............GKIRDILRD.............VF....PVPSAGIHPGIIPNIIADY.GQDVILNSGTGIMDHADGPAAGVKAFFDALDRVKKGEIFNQPGD............................... [uniref90|D8FUJ2 2,3-diketo-5-methylthiopentyl-1-phosphate enolase n=1 Tax=Oscillatoria sp. PCC 6506 RepID=D8FUJ2_9CYAN]
2OEK-B  : ......................AVMATYLLHDE..TDIRKKAEGIALGLTIG............RKHKGEVVAIE.............IVKIAYPTVNFSA.......DLPALLVTTFGKLSLD...GEVRLLDLEFPDEWKRQFPGPRFGIDGIRDRVGVH....RPLLMSIFKGMIGRDLAYLTSELKKQALGVDLVXDDEILFDSELLPFEKRITEGKAALQEVYEQTGKRTLYAVNLTGK.TFALKDKAKRAAEL..........VLLFNVFAYGLDVLQALRED..AVPIMAHPAFSGAVTP...FYGVAPSLWGKLLRLAGADFVL...............LGIARALTD.............PFARAFPVPSAGIHPGLVPLIIRDF.GLDTIVNAGGGIHGHPDGAIGGGRAFRAAIDAVLAGRPLRAAAAENEALQKAIDRWGV................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE ENOLASE]
uniref90: ........................IATYRSHDD..ADFHKKAQGIAVGLTVG............EKHLGKVLSVD.............DIRIAYPDVNFSR.......DIPALLVTIFGKLSMD...GRIKLIDLDVSNEFRSAFPGPKFGLEGVRKLVGVQ....RPLLMSIFKSVIGHDLSGLEEQFYRQALGVDLIKDDEILFENPLTPLEKRVETCMRAARKAKEATGQELLYAVNLTGP.TSQLNANARKAIQA..........ALLFNVLAYGYDALHELSAD..NVPIAAHPSLAGAFYP...HYGIAAPVLGKLMRLAGADLTL...............MAVRDALLD.............SLRKSFPVPSAGIHPGLVPLILRDF.GNDVVVNAGGGVHGHPLGTEAGGQAFRQAIDATLAGQKLAEAAAGHEALQAAITAWGV................. [uniref90|E0IC30 2,3-diketo-5-methylthiopentyl-1-phosphate enolase n=1 Tax=Paenibacillus curdlanolyticus YK9 RepID=E0IC30_9BACL]
3FK4-A  : ......................GIIATYLIHDD...NLEKKAEQIALGLTIG............KQHKGNVIHVE.............IIKIEYPLLNFSP.......DLPAILTTTFGKLSLD...GEVKLIDLTFSDELKKHFPGPKFGIDGIRNLLQVH....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENALTPLTKRIVSGKEVLQSVYETYGHKTLYAVNLTGR.TFDLKENAKRAVQA..........ILLFNVFAYGLDVLQSLAED..PVPIMAHPAVSGAYSA...LYGVSSPLLGKLLRYAGADFSL...............LAISKYLTE...........DASFKKSFSVPSAGIHPGFVPFIVRDF.GKDVVINAGGGIHGHPNGAQGGGKAFRTAIDATLQNKPLHEV..DDINLHSALQIWG.................. [: RUBISCO-LIKE PROTEIN]
uniref90: ......................GIIATYVIHDD...NLTKKAEQIALGLTIG............KQHKGNVVHVE.............IIKIQYPSLNFSP.......DLPAILTTAFGKLSLD...GEIKLIDLTFSDDLKRQFSGPKFGIEEVRKRLHVH....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENALTPLEKRVRSGKEVLQSVYETYGHRTLYAVNITGR.TYDVKENAKRAVNA..........LLLFNAFAYGLDVLQLLAED..NVPIMAHPAISGAYTS...LYGFSHSLLGKLLRYAGADFSL...............LQIAETLTI...........DSHLKRSFPVPSAGIHPGFVPFILRDF.GNDVVINAGGGIHGHPNGAQGGGKAFRAAIDATLQGTPLHEV..DDADLHTALQLWG.................. [uniref90|A7GS60 2,3-diketo-5-methylthiopentyl-1-phosphate enolase n=1 Tax=Bacillus cytotoxicus NVH 391-98 RepID=MTNW_BACCN]

NOTE: To save space, only 20 of 1113 template profile alignments are shown above. The complete set of alignments can be found in the file Homology_7t1c-~_profile.ali. The template profile contains structural alignments of 16 PDB files, which provide safe anchors for the remaining sequence-based alignments (only reliable regions shown).

In the alignment above, 451 of 470 target residues (96.0%) are aligned to template residues. Among these aligned residues, the sequence identity is 81.4% and the sequence similarity is 88.5% ('similar' means that the BLOSUM62 score is > 0). The following 5 loops had to be modeled (only the first of 2 similar loops in the homodimer is listed):

LoopN-terminal anchorLoop sequenceC-terminal anchor
1PVKGGGLFKVAY
3TAFGDDPVKGGGLF
5SSTGTNVEVSTTDDFTRGVDA
7NoneMDQSNR
9REKLGVHKNone

After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).

The resulting half-refined model has been saved as Homology_7t1c-~02_refined050.yob and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals0.546Optimal
Packing 1D-0.581Good
Packing 3D-0.991Good
Overall-0.608Good

Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as Homology_7t1c-~02_refined100.yob, the corresponding Z-scores are listed below:

Check typeQuality Z-scoreComment
Dihedrals0.775Optimal
Packing 1D-0.236Good
Packing 3D-1.148Satisfactory
Overall-0.514Good

Since the overall quality Z-score improved to -0.514 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.

NOTE: 8 residues contained in N- and C-terminal unaligned tails of the homodimeric model have been excluded from the Z-scores in both tables above, since they are not reliable (YASARA does not yet perform ab initio structure prediction) and would have mainly added noise to the result.

The final model for this template and alignment has been saved as Homology_7t1c-~02.yob, and is shown below, together with a plot of its overall quality Z-score, shown per residue:

6.3. Homology model 3/15, based on template 5C2C-~, alignment variant 01

This model is a homodimer, and based on the following profile-profile alignment:

(To improve readability, only up to ten lines of the complete target multiple sequence alignment (MSA) shown above are also displayed here (upside down). The template MSA has been shrunk and focused on structurally aligned PDB entries. The actual target-template alignment can be found in the middle at the line named 'Match'.)

Q08EW6  : .......................................................................................................................NNQGGGDIEHAKIHGIYMPERAIQLFDGPSKDISDMWRILGRPVKDGGYNAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEIQGNQVFSPMNQTIPLVVDAMKRAQDETGQAKLFSANITADDQYEMCARADFILEAFGP..DADKVAFLVDGYVGDPGMITTARSQYPNQYLHYHRAGHGAVNSPKIKRGYTAFVLAKMSRLQGASGAHVGTMGYGKME................................................................................................................................ [uniref90|Q08EW6 Ribulose 1,5-bisphosphate carboxylase/oxygenase large subunit (Fragment) n=1 Tax=uncultured marine bacterium RepID=Q08EW6_9BACT]
Q5DVV5  : ............................................................................................................................................................................IIKPKLGLRPKPFAEACYNFWLGGDFIKNDEPQGNQIWGPIKEVVPLVKDSLVRAQDDTGMAKLFSFNITADDHYEMLHRGEYILETFAEFSE..NIAFLVDGCVGGPGMVTTARRNFPDQFLHYHRAGHGAVTSDQSDRGYNMLVHMKMARLQGASGIHTGTMGYGKMEGAADDKVIAYMLERDSADGLSYHQEWEGMKATTPIICGGMNA...................................................................................... [uniref90|Q5DVV5 Ribulose-1,5-bisphosphate carboxylase oxygenase large subunit (Fragment) n=11 Tax=uncultured prokaryote RepID=Q5DVV5_9ZZZZ]
Q933G7  : ........................................................................................................................................VPPAYLRLFDGPSTTIKDLWRVLGRPVVDGGFIVGTIIKPKLGLRPQPFADACYDFWLGGDFIKNDEPQGNQVFAPFKDTVRAVNDAMRRAQDATGQPKLFSFNITADDHYEMLARGEYILETFGE..NADHVAFLVDGYVAGPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHVGTMGYGKMEGEASDRDSAFMITQDSAEGPYFKQEW...................................................................................................... [uniref90|Q933G7 Form II ribulose 1,5-bisphosphate carboxylase/oxygenase (Fragment) n=5 Tax=Rhodopseudomonas palustris RepID=Q933G7_RHOPA]
F2ZCE9  : .....................................................................................................................................DFYVPPDFLRLFDGPATTISNLWRVLGRPHQNGGFIVGTIVKPKLGLRPRPFADACYDFWLGGDFIKNDEPQGNQTFSPLKETIPLVADAMRRAQDETGEAKLFSANITADDHYEMVARGEFILDTFGEF..ADHVAFLVDGYVAGAAAVTTARRSFPQQYLHYHRAGHGAITSPQSKRGYTAFVHCKMARLQGASGIHTGTMSFGKMEGEAADRAIAFMLEQDSADGPYFHQEWHGMNPTTSIISG.......................................................................................... [uniref90|F2ZCE9 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=1 Tax=uncultured bacterium RepID=F2ZCE9_9BACT]
F2ZCD0  : ......................................................................................................................GNNQGMGDIANAQMQDFYVPPAMLALFDGPAKSINDLWTLLGRDNENGGYIAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEPQGNQVFCPLKKVLPLVHDAMKRAQDETGEAKLFSLNITADDHYEMCARADFGLETFGE..DAPRLAFLVDGFVGGPGMVTTARRQYSSQYLHYHRAGHGMITSPSSKRGYTAYILAKMSRLMGASGIHVGTMGYGKMEGGADDKIIAYMIERDECQGPFYYQKWHGMKPTTPIVSGGM........................................................................................ [uniref90|F2ZCD0 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=4 Tax=uncultured bacterium RepID=F2ZCD0_9BACT]
F5BZE6  : ......................................................................................................................GNNQGMGDVEYAKMIDFYMARSLLTLFDGPAMNITDMWRVLGRPQVNGGMVVGTIIKPKLGLRPKPFADACYMFWMGGDFIKNDEPQGNQVFAPTREIIPLVAEAMERAQQETGEAKIFSANITADDPFEMIRRGEFILEAFGK..NASHVAFLVDGYVGGPSAVTLCRRYFPNQFLHYHRAGHGAVTSNQSKRGYTVLTHMKMSRLQGASGIHTGTMGYGKMEGDKNEKMVAYMIERDEAMGVYYNQPWHGMTATTPIISGGMNALR.................................................................................... [uniref90|F5BZE6 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II (Fragment) n=1 Tax=alpha proteobacterium LM-5 RepID=F5BZE6_9PROT]
Q9FPW1  : LDQSSRYADLSLDEATLVKNGKHVLVAYIMKPKAGYDYLATAAHFAAESSTGTNVNVCTTDDFTKSVDALVYYIDPDSEE.........MKIAYPTLLFDRNIIDGRGMMCSFLTLAIGNNQGMGDVEYGKIYDFYLPPSFLRLYDGPAVNVEDMWRILGKGTSNGGLVDGTIIKPKLGLQPNPFGEACYSFWQGGDFIKNDEPQGNQVFCQMNECIPEVVKAMRACVKETGSSKLFSANITADDPEEMIARGKYIMSQFGPLSE..NCAFLVDGYVAGGTAVTCCRRNFPKQFLHYHRAGHGSVTSPQTQRGYTAFVHTKISRVIGASGIHVGTMSFGKMEGDASDKNIAYMLQDDEADGPYYRQEWQGMKETTPIISGGMNALRLPAFFENLGHSNVILTAGGGSFGHKDGPKIGAISCRQGEEAWKSLSDVIEYAKTHEEIKGAFLTFQKDADQIYPGWKEKLG... [uniref90|Q9FPW1 Ribulose 1,5-bisphosphate carboxylase oxygenase large subunit n=1 Tax=Symbiodinium sp. RepID=Q9FPW1_SYMSP]
E6VVI6  : .DQTSRYVNFDLKEDQLIADGNHVLCAYIYKPANGYGNVEVAAHFAAESSTGTNVEVCTTDDFTKGVDALVYEVSDASNGDS......LMKIAYPVELFDRNIIDGRAMLASFLTLCIGNNQGMGDVAYAKMHDFYVPRQYLELFDGPSKNIADFWRMLGRPTENGGMIAGTIVKPKLGLRPKPFADACYHFWLGGDFVKNDEPQGNQVFAPLKETITAVADAMRRAQDETGEAKIFSANITADDPREMIARGEFILNAFGE..NASRVAFLVDGYVAGPTAITTARRNFPNQFLHYHRAGHGAVTSPQAKRGYTAFVLSKMSRLQGASGIHTGTMGFGKMEGEMADKSMAYMIEREEAQGPYFKQKWYGMKATTPMISGGMNALRLPGFFDNLGHSNICQTSGGGAFGHLDGPTAGALSLRQSHDAWIQGVNLLDYAKEHNELARAFESFPGDADRFYPTWRHQL.... [uniref90|E6VVI6 Ribulose-bisphosphate carboxylase n=1 Tax=Desulfovibrio aespoeensis Aspo-2 RepID=E6VVI6_DESAO]
Q8RTI1  : MDQSNRYADLSLKEDDLIKGGNHVLVAYLMKPKTGYGYLEAAAHFSAESSTGTNVEVSTTDDFTKGVDALVYEIDEAK.........EIMKIAYPVDLFDRNITDGRAMIVSFLTLAIGNNQGMGDIAYAKMLDFYVPQKYLRLFDGPSKDISDLWRILGRPVVNGGYIAGTIIKPKLGLRPKPFAEAAYQFWLGGDFIKNDEPQGNQVFSPMRETIPLVYDSMKRAMDETGEAKLFSANITADDHYEMMARGEFILNTFGP..DADKVAFLVDGYVGGPGMVTTARRHFANQYLHYHRAGHGAVTSPSAKRGYTAFVLAKMSRLQGASGIHVGTMGYGKMEGDATDKNIAYMIERDSADGPFYHQEWYGMKPTTPIISGGMNALRLPGFFENLGHANLINTSGGGSYGHIDSPAAGAISLRQAYECWQQGADPIEFAKEHKEFARAFESFPGDADTIFPGWREKLGVHK [uniref90|Q8RTI1 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II n=1 Tax=magnetite-containing magnetic vibrio RepID=Q8RTI1_9PROT]
Q0F2Z8  : MDQSNRYADLSLNEADLIAGGKHLLVAYKLIPAKGYGFLEVAAHIAAESSTGTNVEVSTTDDFTRGVDALVYDIDETAFGDEGVTGGGLMKVAYPVELFDPNLIDGHYNVSHMWSLILGNNQGMGDHEGLRMLDFMVPECMIRKFDGPSAGIADLWKVLGRPEVDGGYISGTIIKPKLGLRPEPFAKACLDFWLGGDFIKNDEPQANQPFCPMKVVIPKVAEAMDRAQQETGQAKLFSANATADYHGECVARGEYILSEFAKYGNEKHVAFLIDGFVTGPAGVTTARRAFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLARLQGASGIHTGTMGYGKMEGHGKETVLAYMLERDECMGHYFNQKWYGMKPTAPIISGGMNALRLPGFFENLGHGNVINTCGGGSFGHIDSPAAGGKSLDQAYDCWKSGTDPIEYAKTHGEFARAFESFPGDADKLYPGWRDKLGVHK [uniref90|Q0F2Z8 Ribulose-bisphosphate carboxylase n=1 Tax=Mariprofundus ferrooxydans PV-1 RepID=Q0F2Z8_9PROT]
SecStr  : CCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCEEECCCCCCHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCEEEECCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEECCCCCCHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCHHCCCCCCCEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHHHHCCCC [Secondary structure predicted by PsiPred]
Target  : MDQSNRYANLNLKEEDLIKNGKHLLVAYKLIPAKGHGFLEVAAHVAAESSTGTNVEVSTTDDFTRGVDALVYEIDETAFGDDPVKGGGLFKVAYPVELFDPNLTDGTYNISHMWSLILGNNQGMGDHQGLRMLDFLVPEMMVRKFDGPSANISNLWKVLGRSETDGGYIAGTIIKPKLGLRPEPFAKACYDFWLGGDFIKNDEPQANQPFCPMEVVMPKVAEAMDRAQQATGQAKLFSANITADYYKEMIHRGDFVLETFAKYNSASHVAFLVDGFVTGPAGVTTARREFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLVRLMGASGMHTGTMGYGKMEGHGKETVLAYMLERDECQGPYFYQKWYGMKATTPIISGGMNALRLPGFFQNLGHGNVINTCGGGAFGHIDSPAAGGISLGQAYDCWKSGSDPIEYAKTHKEFARAFESFPKDGDKLFAGWREKLGVHK
Match   :   QSNRYA:L:LKEEDLIK:G:H|LVAY | PA G G|LE:AAH|AAESSTG            |GVDALVY IDE:          G|:KVAYP |LFD N:TDG   I  : :L |GNNQGMGD  :L:M DF VP  M:: FDGP: :IS:LW||LGR   DGGYI:GTIIKPKLGLRPEPFAKA:Y:FWLGGDFI:NDEPQ:NQ FCP:: V|P V |:| RAQ: TGQAKLFS NITAD | EM  R:DF:LETF:   :A: VAFLVDGFV GP: VTTARR||P: |LH|HRAGHG VTS :S  G   :   K| RL:GASG:H:GTMGYGKMEG   | ||AYM|ERD:C GP|||Q:WYGMK TTPIISGGMNALRLPGFF|NLGHGNVINT:GGG:|GHIDSPAAG:|SL QAY|CWK:G:DPIE|AK HKEFARAFESFPKD:DKLF GWREKLGVHK
Template: ..QSNRYADLSLKEEDLIKGGNHILVAYTMEPAAGVGYLEAAAHIAAESSTG............KGVDALVYFIDEA.........KGIMKVAYPNDLFDRNVTDGRVMIVSFLTLCIGNNQGMGDIANLQMQDFYVPPRMLQLFDGPAKDISDLWRILGRPVKDGGYISGTIIKPKLGLRPEPFAKAAYQFWLGGDFIXNDEPQGNQVFCPIKKVLPLVYDSLKRAQDETGQAKLFSMNITADDHYEMCARADFALETFG...DADKVAFLVDGFVGGPGMVTTARRQYPSQYLHYHRAGHGMVTSPSSKRGYTAFVLAKMSRLQGASGIHVGTMGYGKMEGGKDDRIIAYMIERDSCTGPFYHQEWYGMKPTTPIISGGMNALRLPGFFENLGHGNVINTAGGGSYGHIDSPAAGAVSLRQAYECWKAGADPIEWAKEHKEFARAFESFPKDADKLFPGWREKLGVHK
SecStr  : ..HHHHHCTTTTHHHHHHHHCCCEEEEEEEECTTTTHHHHHHHHHHHHHCCC............GGCCCEEEEEECC.........CEEEEEEETTTTCCCCCCCCCCHHHHHHHHHHGGGGCTTTTEEEEEEEEECHHHHHHCCCCCCCCHHHHHHHHHCCCCCCCCEEEECCCCCCCCHHHHHHHHHHHHHHCCEEEEETTTTCCTTTTHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCHHHHHHHHHHHHHHHHH...TTTEEEEEEHHHHHCHHHHHHHHHHHCCCEEEEETTTTCCCCTTTTCCCCHHHHHHHHHHHHHCEEEEECTTTTCCCCCTTTTHHHHHHHHCEEEECCCEEEEETTTCCCEEEECCCCCCCHHHHHHHHHHCCCEEEEEHHHHHHCCCHHHHHHHHHHHHHHHHHHCCHHHHHHCCHHHHHHHHHHCHHHHHHHHCHHHHHHHCCC [Secondary structure assigned by YASARA]
1RSC-G  : ....LTYYTPDYTP.....KDTDLLAAFRFSPQPGVPADEAGAAIAAESST.............DRYKGKCYHIEP............FAFIAYPLDLFEE.......SVTNILTSIVGNVFGFKAIRSLRLEDIRFPVALVKTFQGPPHGIQVERDLLNKY....RPMLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKSQAETGEIKGHYLNVTAPTCEEMMKRAEFAKEL..........IIMHDFLTAGFTANTTLAKWCRGVLLHIHRAMHAVIDR...NHGIHFRVLAKCLRLSGGDHLH..............TLGFVDLMREDHIEA.FFTQDWASMPGVLPVASGGIHVWHMPALVEIF.GDDSVLQFGGGTLGHPWGNAPGATANRVALEACVQ...LREAGKWSPELAAALDLW................... [: RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (LARGE]
1GEH-B  : ..........GYEP.......RDIIAVFRVTPAEGYTIEQAAGAVAAESST.............ADLSAKAYDFHD............IVRIAYPFHAFEE.......NLPGLLASIAGNIFGMKRVKGLRLEDLYFPEKLIREFDGPAFGIEGVRKMLEIK....RPIYGVVPKPKVGYSPEEFEKLAYDLLSNADYMKDDENLTSPWYNRFEERAEIMAKIIDKVENETGEKKTWFANITAD.LLEMEQRLEVLADL..........HAMVDVVITGWGALRYIRDLAAGLAIHGHRAMHAAFTR...YHGISMFVLAKLYRLIGIDQLH..............VIQNARILRESHYK...LEQKFYSIKAAFPTSSGGLHPGNIQPVIEAL.GTDIVLQLGGGTLGHPDGPAAGARAVRQAIDAIMQGIPLDEYAKTHKELARALEKW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE]
1SVD-A  : .....TYWMPEYTP.....LDSDILACFKITPQPGVDREEAAAAVAAESSTG............DYYKGRAYRIED............YAFIAYPIDLFEE.......SVVNVFTSLVGNVFGFKAVRGLRLEDVRFPLAYVKTCGGPPHGIQVERDKMNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFMRWRDRFLFVQDATETAEAQTGERKGHYLNVTAPTPEEMYKRAEFAKEI..........IIMHDYITGGFTANTGLAKWCQGVLLHIHRAMHAVIDR...NHGIHFRVLTKILRLSGGDHLH..............TLGWIDLLRESFIP..FFDQDWGSMPGVFAVASGGIHVWHMPALVNIF.GDDSVLQFGGGTLGHPWGNAAGAAANRVALEACVE...LTAAAQHSPELKIAMETW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE]
2YBV-A  : ......YYTPDYTP.....KDTDILAAFRVTPQPGVPFEEAAAAVAAESSTG............DRYKGCCYDIEP............IAYIAYPLDLFEE.......SVTNMLTSIVGNVFGFKALKALRLEDLRIPVAYLKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKAQAETGEIKGHYLNVTAPTCEEMLKRAEFAKEL..........IIMHDFLTAGFTANTTLSKWCRGMLLHIHRAMHAVMDR...NHGIHFRVLAKCLRMSGGDHIH..............TLGFVDLLRENYIE..YFTQDWASMPGVMAVASGGIHVWHMPALVDIF.GDDAVLQFG.....HPWGNAPGATANRVALEACIQ...IREAARWSPELAAAC...................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN]
1BXN-C  : ....MGYWDGDYVP.....KDTDLLALFRITPQDGVDPVEAAAAVAGESST.............DMYRAKAYRVDP............FCYVAYDLSLFEE.......SIANLTASIIGNVFSFKPIKAARLEDMRFPVAYVKTFAGPSTGIIVERERLDKF....RPLLGATTKPKLGLSGRNYGRVVYEGLKGLDFMKDDENINSQPFMHWRDRFLFVMDAVNKASAATGEVKGSYLNVTAGTMEEMYRRAEFAKSL..........IIMVD.LIVGWTCIQSMSNWCRDMILHLHRAGHGTYTR...NHGVSFRVIAKWLRLAGVDHMH..............VQGYYNVCRDAYTQ..FFDQDWASLRKVMPVASGGIHAGQMHQLIHLF.GDDVVLQFGGGTIGHPQGIQAGATANRVALEAMVL...LRDAARWCGPLRAALDTW................... [: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)]
1EJ7-L  : .....TYYTPEYQT.....KDTDILAAFRVTPQPGVPPEEAGAAVAAESSTG............DRYKGRCYRIER............IAYVAYPLDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENVNSQPFMRWRDRFLFCAEALYKAQAETGEIKGHYLNATAGTCEEMIKRAVFAREL..........IVMHDYLTGGFTANTSLAHYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHIH..............TLGFVDLLRDDFVE..YFTQDWVSLPGVLPVASGGIHVWHMPALTEIF.GDDSVLQFGGGTLGHPWGNAPGAVANRVALEACVK...IREACKWSPELAAACEVW................... [: RUBISCO (LARGE SUBUNIT)]
1IWA-C  : ....MGYWNPDYQV.....KDTDVLALFRVTPQPGVDPIEAAAAVAGESST.............DLYRAKAYKVDQ............FAYIAYELDLFEE.......SIANLTASIIGNVFGFKAVKALRLEDMRLPLAYLKTFQGPATGVILERERLDKF....RPLLGCTTKPKLGLSGKNYGRVVYEALKGLDFVKDDENINSQPFMRWRERYLFTMEAVNKASAATGEVKGHYLNVTAATMEEMYARANFAKEL..........IIMID.LVIGYTAIQTMAKWARDMILHLHRAGNSTYSR...NHGMNFRVICKWMRMAGVDHIH..............TRGFYKTLLLPKLE..FFDMEWASLRKVMPVASGGIHAGQMHQLIHYLG.EDVVLQFGGGTIGHPDGIQAGATANRVALEAMIL...LREAAKTCGALRTALDLW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE]
1TEL-B  : .....GFFAS...........QYLVLDYYLESV..GDIETALAHFCSEQSTA............RVHAAKVIDYEV............RVTIAHPHCNFGP.......KIPNLLTAVCGETYFTPGVPVVKLMDIHFPDTYLADFEGPKFGIEGLRDILNAH....RPIFFGVVKPNIGLSPGEFAEIAYQSWLGLDIAKDDEMLADVTWSSIEERAAHLGKARRKAEAETGEPKIYLANITDE.VDSLMEKHDVAVRN..........ALLINALPVGLSAVRMLSNYT.QVPLIGHFPFIASFSR...KYGIHSKVMTKLQRLAGLDAVI..............VLENVIECTKP..........MGRIKPCLPVPGGSDSALTLQTVYEKVGNVDFGFVPGRGVFGHPMGPKAGAKSIRQAWEAIEQGISIETWAETHPELQAMVDQ.................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE, LARGE SUBUNIT]
2D69-A  : .....DFVDLNYEP.....GRDELIVEYYFEPN.GVSPEEAAGRIASESSIG............KRSMAKVFYLEK............IAKIAYPLTLFEE.......SLVQLFSAVAGNVFGMKALKNLRLLDFHPPYEYLRHFKGPQFGVQGIREFMGVK....RPLTATVPKPKMGWSVEEYAEIAYELWSGIDLLKDDENFTSFPFNRFEERVRKLYRVRDRVEAETGETKEYLINITGP.VNIMEKRAEMVANE..........YVMIDIVVAGWSALQYMREVTEGLAIHAHRAMHAAFTR...RHGITMLALAKAARMIGVDQIH..............IKRINDFLLS...........WEHIRPVFPVASGGLHPGLMPELIRLF.GKDLVIQAGGGVMGHPDGPRAGAKALRDAIDAAIEGVDLDEKAKSSPELKKSLREV................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE]
2QYG-D  : .....GFYAK...........NYIELDFDFECA..GDPHEAAAHLCSEQSTA............PRFAAKVLELSA............RVTIAHPHGNF........AKIPNLLSAVCGEVFFSPGIPLIRLQDIRFPEPYLAAFDGPRFGIAGVRERLQAF....RPIFFGVIKPNIGLPPQPFAELGYQSWTGLDIAKDDEMLADVDWCPLAERAALLGDACRRASAETGVPKIYLANITDE.VDRLTELHDVAVAN..........ALLINAMPVGLSAVRMLRKHA.TVPLIAHFPFIAAFSR...NYGIHSRVMTRLQRLAGFDVVI..............VLDCIRACLE...........MGPIKPCLPVPGGSDSAATLENVYRKVGSADFGFVPGRGVFGHPMGPAAGATSIRQAWDAIAAGIPVPDHAASHPELAAALRAF................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE-LIKE PROTEIN 2]
2V67-A  : ....LTYYTPDYVV......DTDILAAFRMTPQPGVPPEECGAAVAAESST.............DRYKGRCYDIEP............IAYVAYXIDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFVGXPHGIQVERDKLNKY....RGLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTXDDENVNSQPFMRWRDRFLFVAEAIYKAQAETGEVKGHYLNATAGTCEEMMKRAVXAKEL..........IIMHDYLTGGFTANTSLAIYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHLH..............ILGFVDLMRDDYVE..YFTQDWXSMPGVMPVASGGIHVWHMPALVEIF.GDDACLQFGGGTLGHPWGNAPGAAANRVALEACTQ...IRSACKWSPELAAACEVW................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN]
3NWR-A  : ....................EDTLEADYLIET..PLDPARVADVMAGEQSSG............ARSRASVLRIEE............RITLSFPLANI.........NLPTLAATVAGNLYDLGEVTGVRLLSLRLPASYRARFELPRHGVAGTRALTDVK....RPMIGTIIKPNVGLSAAETAALVRELCEAVDFIXDDEVCANPAHAPLAERVRAVMSEVRRYRERSGRPVMVAFNITDD.LDAMRRHAELVERE..........CVMASINWCGFSAIQSLRRTT.PLVLHAHRNGYGMMSR...ALGMSFQAYQTLWRLSGVDHMH..............VIESARDCATP...............AVLPAFSSGQWAGTVQATFDAVRSTDLLFMSGGGILAHPDGPAAGVTSVRQAWAAVQAGTPLPVYAEHMPELRRALAFF................... [: A RUBISCO-LIKE PROTEIN]
3QFW-B  : ......................RIVATYHIAS.....IEQRALALAIEQSVE.............NIVGRVEDVAE............AVRIGLAAATAP.......AEPGQLLNMLFGNSSIQPD...IALADVELPAHYLTAFGGPRVGLAGIRTLTGAQ....RALTASALKP.QGLSPAALASIAHQLALGVDLIKDDHGLADQAFSPFAERAAAVGKAVREANAARGGRTLYAPNISG.TLDDMRRQLGVIRDE..........AVLVAPMIVGVSNFHAIVKEAAGLVVVAHPAMAGAA........IAAPLLGRLFRLFGADATV..............CLALAQAARD...........FGKLNACIPTPAGGIMLQRVNELLRFYG.QDVMLLI..........LTEQASRFVNKVADYGQR....................................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE]
uniref90: ......................RIIATYRVTS.....IADRAQGLAIEQSVE.............GIVGRVALIDQ............AVRVALAAATAP.......AEPGQLLNMLFGNASIQPD...VALVDVELPPAYLAAFGGPKLGLDGIRARTGVH....RALTASALKP.QGLAPAALAAIARQLAEGVDLIKDDHGLADQAYSPFAARIAAVGRAVDAANQASGRRALYAPHVSG.SLDEMRRQLDLIRAE..........ALMMMPMIVGLSNFHVIAREAEGLVVLAHPALSGAT........IAPPLLGKLFRLLGADATV..............CRALADAARG...........WGGLKPCLPVPAGGIAIDRVEELLSFYG.RDVMLLI..........LGAEAARFVAEVAAHG......................................... [uniref90|Q2IV37 Ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit n=1 Tax=Rhodopseudomonas palustris HaA2 RepID=Q2IV37_RHOP2]
2ZVI-A  : ......................ELLATYLLT.....DTEKKAEQIATGLTVG............QKHKGRVIKVEE............VITIAYPEINFSQ.......DIPALLTTVFGKLSL...DGKIKLIDLHFSEAFKRALPGPKFGVYGIRKLLGE.....RPLLMSIFKGVIGRDLSDIKEQLRQQALGVDLIKDDEIFFETGLAPFETRIAEGKQILKETYEQTGHKTLYAVNLTGR.TADLKDKARRAAEL..........ALLFNVFAYGLDVMQGLAED..PVPIMAHPAVSGAFTS...FYGFSHALLGKLNRYCGADFSL..............ALAIHEECVR.............AFNQTFAVPSAGIHPGMVPLLMRDF.GIDHIINAGGGVHGHPNGAQGGGRAFRAIIDAVLEAQPIDEKAEQCKDLKLALDKWGK................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE]
uniref90: ......................ELLATYILA.....DAEKRAEQIAIGLTVG............KKHKGRVVNVEE............TVTIAYPEANFTN.......DIPAVLTTVFGKLSL...DGKIKLADLEFSRSFKQSLPGPKFGVYGIRKKIGE.....RPLLMSIFKGVIGRDMEDLKEQLRQQALGVDLIKDDEILFETGSAPFEKRITEGKKVLEEAFEETGRKTLYAVNLTGR.TMELKAKARKAAEL..........VLLLNVFAYGLDVLQSFAED..PLPIMAHPAVSGALTS...HYGFSHSLLGKLNRYAGADFSL..............ALAIYDECTK.............VFKPTFAVPSAGIHPGMVPLLMKDF.GIDHIINAGGGIHGHPNGAAGGGRAFRAVIDAVLEAEPVEEKAKRSPDLKLALEKWGR................. [uniref90|Q65KJ8 2,3-diketo-5-methylthiopentyl-1-phosphate enolase n=2 Tax=Bacillus RepID=MTNW_BACLD]
2OEK-B  : ......................AVMATYLLHDE..TDIRKKAEGIALGLTIG............RKHKGEVVAIEE............IVKIAYPTVNFSA.......DLPALLVTTFGKLSLD...GEVRLLDLEFPDEWKRQFPGPRFGIDGIRDRVGVH....RPLLMSIFKGMIGRDLAYLTSELKKQALGVDLVXDDEILFDSELLPFEKRITEGKAALQEVYEQTGKRTLYAVNLTGK.TFALKDKAKRAAEL..........VLLFNVFAYGLDVLQALRED..AVPIMAHPAFSGAVTP...FYGVAPSLWGKLLRLAGADFVL..............ALGIARALTD.............PFARAFPVPSAGIHPGLVPLIIRDF.GLDTIVNAGGGIHGHPDGAIGGGRAFRAAIDAVLAGRPLRAAAAENEALQKAIDRWGV................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE ENOLASE]
uniref90: .......................ILVTYLTQAK...DLNKKAQAIAVGMTVG............APYLGEAVSATP............LITVSYPTRNFTA.......DIPSLLTGIFGKLSMD...GKIKLVDIVFPESFLQAFPGPKFGIDGLRERLGAH....RPLLMSIFKSCLGLPFDDLKTQFRAQALGVDLVKDDEIFFADDRAPFIERIKAFKQIAQETEAETGKPVLYAANLTGP.VHELNEKAKRAVEA..........CLLFNVLAFGFDALHRLAAD..HVPIMAHPALAGAYYP...DYGIATPLLGTLMRVAGADLVL..............ALQLAKHLTD.............GVRRSFPVPSAGIHPGLVPQLYQDF.GLDQIVNAGGGIHGHPGGATAGAKAFVAAIEAVTAGRTLEEASSESQELAIALEKWG.................. [uniref90|C0ZL40 2,3-diketo-5-methylthiopentyl-1-phosphate enolase n=1 Tax=Brevibacillus brevis NBRC 100599 RepID=C0ZL40_BREBN]
3FK4-A  : ......................GIIATYLIHDD...NLEKKAEQIALGLTIG............KQHKGNVIHVEE............IIKIEYPLLNFSP.......DLPAILTTTFGKLSLD...GEVKLIDLTFSDELKKHFPGPKFGIDGIRNLLQVH....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENALTPLTKRIVSGKEVLQSVYETYGHKTLYAVNLTGR.TFDLKENAKRAVQA..........ILLFNVFAYGLDVLQSLAED..PVPIMAHPAVSGAYSA...LYGVSSPLLGKLLRYAGADFSL..............ALAISKYLTE...........DASFKKSFSVPSAGIHPGFVPFIVRDF.GKDVVINAGGGIHGHPNGAQGGGKAFRTAIDATLQNKPLHEV..DDINLHSALQIWG.................. [: RUBISCO-LIKE PROTEIN]
uniref90: ......................GIIATYLIHDD...NLEKKAEQIALGLTIG............KQHKGNVLHVEE............IIKIEYPLLNFSP.......DLPAILTTTFGKLSLD...GEVKLIDLTFSDELKKHFPGPKFGIDGIRNLLQVH....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENALTPLTNRIVSGKEVLQSVYETYGHKTLYAVNVTGR.TFDLKENAKRAVQA..........ILLFNVFAYGLDVLQSLAED..PVPIMAHPAVSGAYSA...LYGISSPLLGKLLRYAGADFSL..............ALAISKYLTE...........DVFFKKSFSVPSAGIHPGFVPFIIRDF.GKDVVINAGGGIHGHPNGAQGGGKAFRTAIDATLQNKPLHEV..DDINLHSALQIWG.................. [uniref90|C3P745 2,3-diketo-5-methylthiopentyl-1-phosphate enolase n=71 Tax=Bacillus cereus group RepID=MTNW_BACAA]

NOTE: To save space, only 20 of 1107 template profile alignments are shown above. The complete set of alignments can be found in the file Homology_5c2c-~_profile.ali. The template profile contains structural alignments of 16 PDB files, which provide safe anchors for the remaining sequence-based alignments (only reliable regions shown).

In the alignment above, 444 of 470 target residues (94.5%) are aligned to template residues. Among these aligned residues, the sequence identity is 68.9% and the sequence similarity is 80.2% ('similar' means that the BLOSUM62 score is > 0). The following 4 loops had to be modeled (only the first of 2 similar loops in the homodimer is listed):

LoopN-terminal anchorLoop sequenceC-terminal anchor
1LETFAKYNSASHV
3EIDETAFGDDPVKGGGLFK
5ESSTGTNVEVSTTDDFTRGVDA
7NoneMDQSNRY

After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).

The resulting half-refined model has been saved as Homology_5c2c-~01_refined050.yob and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals0.319Optimal
Packing 1D-0.890Good
Packing 3D-1.084Satisfactory
Overall-0.805Good

Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as Homology_5c2c-~01_refined100.yob, the corresponding Z-scores are listed below:

Check typeQuality Z-scoreComment
Dihedrals0.553Optimal
Packing 1D-0.398Good
Packing 3D-1.315Satisfactory
Overall-0.686Good

Since the overall quality Z-score improved to -0.686 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.

NOTE: 4 residues contained in N- and C-terminal unaligned tails of the homodimeric model have been excluded from the Z-scores in both tables above, since they are not reliable (YASARA does not yet perform ab initio structure prediction) and would have mainly added noise to the result.

The final model for this template and alignment has been saved as Homology_5c2c-~01.yob, and is shown below, together with a plot of its overall quality Z-score, shown per residue:

6.4. Homology model 4/15, based on template 5C2C-~, alignment variant 02

This model is a homodimer, and based on the following profile-profile alignment:

(To improve readability, only up to ten lines of the complete target multiple sequence alignment (MSA) shown above are also displayed here (upside down). The template MSA has been shrunk and focused on structurally aligned PDB entries. The actual target-template alignment can be found in the middle at the line named 'Match'.)

Q08EW6  : .......................................................................................................................NNQGGGDIEHAKIHGIYMPERAIQLFDGPSKDISDMWRILGRPVKDGGYNAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEIQGNQVFSPMNQTIPLVVDAMKRAQDETGQAKLFSANITADDQYEMCARADFILEAFGP..DADKVAFLVDGYVGDPGMITTARSQYPNQYLHYHRAGHGAVNSPKIKRGYTAFVLAKMSRLQGASGAHVGTMGYGKME................................................................................................................................ [uniref90|Q08EW6 Ribulose 1,5-bisphosphate carboxylase/oxygenase large subunit (Fragment) n=1 Tax=uncultured marine bacterium RepID=Q08EW6_9BACT]
Q5DVV5  : ............................................................................................................................................................................IIKPKLGLRPKPFAEACYNFWLGGDFIKNDEPQGNQIWGPIKEVVPLVKDSLVRAQDDTGMAKLFSFNITADDHYEMLHRGEYILETFAEFSE..NIAFLVDGCVGGPGMVTTARRNFPDQFLHYHRAGHGAVTSDQSDRGYNMLVHMKMARLQGASGIHTGTMGYGKMEGAADDKVIAYMLERDSADGLSYHQEWEGMKATTPIICGGMNA...................................................................................... [uniref90|Q5DVV5 Ribulose-1,5-bisphosphate carboxylase oxygenase large subunit (Fragment) n=11 Tax=uncultured prokaryote RepID=Q5DVV5_9ZZZZ]
Q933G7  : ........................................................................................................................................VPPAYLRLFDGPSTTIKDLWRVLGRPVVDGGFIVGTIIKPKLGLRPQPFADACYDFWLGGDFIKNDEPQGNQVFAPFKDTVRAVNDAMRRAQDATGQPKLFSFNITADDHYEMLARGEYILETFGE..NADHVAFLVDGYVAGPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHVGTMGYGKMEGEASDRDSAFMITQDSAEGPYFKQEW...................................................................................................... [uniref90|Q933G7 Form II ribulose 1,5-bisphosphate carboxylase/oxygenase (Fragment) n=5 Tax=Rhodopseudomonas palustris RepID=Q933G7_RHOPA]
F2ZCE9  : .....................................................................................................................................DFYVPPDFLRLFDGPATTISNLWRVLGRPHQNGGFIVGTIVKPKLGLRPRPFADACYDFWLGGDFIKNDEPQGNQTFSPLKETIPLVADAMRRAQDETGEAKLFSANITADDHYEMVARGEFILDTFGEF..ADHVAFLVDGYVAGAAAVTTARRSFPQQYLHYHRAGHGAITSPQSKRGYTAFVHCKMARLQGASGIHTGTMSFGKMEGEAADRAIAFMLEQDSADGPYFHQEWHGMNPTTSIISG.......................................................................................... [uniref90|F2ZCE9 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=1 Tax=uncultured bacterium RepID=F2ZCE9_9BACT]
F2ZCD0  : ......................................................................................................................GNNQGMGDIANAQMQDFYVPPAMLALFDGPAKSINDLWTLLGRDNENGGYIAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEPQGNQVFCPLKKVLPLVHDAMKRAQDETGEAKLFSLNITADDHYEMCARADFGLETFGE..DAPRLAFLVDGFVGGPGMVTTARRQYSSQYLHYHRAGHGMITSPSSKRGYTAYILAKMSRLMGASGIHVGTMGYGKMEGGADDKIIAYMIERDECQGPFYYQKWHGMKPTTPIVSGGM........................................................................................ [uniref90|F2ZCD0 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=4 Tax=uncultured bacterium RepID=F2ZCD0_9BACT]
F5BZE6  : ......................................................................................................................GNNQGMGDVEYAKMIDFYMARSLLTLFDGPAMNITDMWRVLGRPQVNGGMVVGTIIKPKLGLRPKPFADACYMFWMGGDFIKNDEPQGNQVFAPTREIIPLVAEAMERAQQETGEAKIFSANITADDPFEMIRRGEFILEAFGK..NASHVAFLVDGYVGGPSAVTLCRRYFPNQFLHYHRAGHGAVTSNQSKRGYTVLTHMKMSRLQGASGIHTGTMGYGKMEGDKNEKMVAYMIERDEAMGVYYNQPWHGMTATTPIISGGMNALR.................................................................................... [uniref90|F5BZE6 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II (Fragment) n=1 Tax=alpha proteobacterium LM-5 RepID=F5BZE6_9PROT]
Q9FPW1  : LDQSSRYADLSLDEATLVKNGKHVLVAYIMKPKAGYDYLATAAHFAAESSTGTNVNVCTTDDFTKSVDALVYYIDPDSEE.........MKIAYPTLLFDRNIIDGRGMMCSFLTLAIGNNQGMGDVEYGKIYDFYLPPSFLRLYDGPAVNVEDMWRILGKGTSNGGLVDGTIIKPKLGLQPNPFGEACYSFWQGGDFIKNDEPQGNQVFCQMNECIPEVVKAMRACVKETGSSKLFSANITADDPEEMIARGKYIMSQFGPLSE..NCAFLVDGYVAGGTAVTCCRRNFPKQFLHYHRAGHGSVTSPQTQRGYTAFVHTKISRVIGASGIHVGTMSFGKMEGDASDKNIAYMLQDDEADGPYYRQEWQGMKETTPIISGGMNALRLPAFFENLGHSNVILTAGGGSFGHKDGPKIGAISCRQGEEAWKSLSDVIEYAKTHEEIKGAFLTFQKDADQIYPGWKEKLG... [uniref90|Q9FPW1 Ribulose 1,5-bisphosphate carboxylase oxygenase large subunit n=1 Tax=Symbiodinium sp. RepID=Q9FPW1_SYMSP]
E6VVI6  : .DQTSRYVNFDLKEDQLIADGNHVLCAYIYKPANGYGNVEVAAHFAAESSTGTNVEVCTTDDFTKGVDALVYEVSDASNGDS......LMKIAYPVELFDRNIIDGRAMLASFLTLCIGNNQGMGDVAYAKMHDFYVPRQYLELFDGPSKNIADFWRMLGRPTENGGMIAGTIVKPKLGLRPKPFADACYHFWLGGDFVKNDEPQGNQVFAPLKETITAVADAMRRAQDETGEAKIFSANITADDPREMIARGEFILNAFGE..NASRVAFLVDGYVAGPTAITTARRNFPNQFLHYHRAGHGAVTSPQAKRGYTAFVLSKMSRLQGASGIHTGTMGFGKMEGEMADKSMAYMIEREEAQGPYFKQKWYGMKATTPMISGGMNALRLPGFFDNLGHSNICQTSGGGAFGHLDGPTAGALSLRQSHDAWIQGVNLLDYAKEHNELARAFESFPGDADRFYPTWRHQL.... [uniref90|E6VVI6 Ribulose-bisphosphate carboxylase n=1 Tax=Desulfovibrio aespoeensis Aspo-2 RepID=E6VVI6_DESAO]
Q8RTI1  : MDQSNRYADLSLKEDDLIKGGNHVLVAYLMKPKTGYGYLEAAAHFSAESSTGTNVEVSTTDDFTKGVDALVYEIDEAK.........EIMKIAYPVDLFDRNITDGRAMIVSFLTLAIGNNQGMGDIAYAKMLDFYVPQKYLRLFDGPSKDISDLWRILGRPVVNGGYIAGTIIKPKLGLRPKPFAEAAYQFWLGGDFIKNDEPQGNQVFSPMRETIPLVYDSMKRAMDETGEAKLFSANITADDHYEMMARGEFILNTFGP..DADKVAFLVDGYVGGPGMVTTARRHFANQYLHYHRAGHGAVTSPSAKRGYTAFVLAKMSRLQGASGIHVGTMGYGKMEGDATDKNIAYMIERDSADGPFYHQEWYGMKPTTPIISGGMNALRLPGFFENLGHANLINTSGGGSYGHIDSPAAGAISLRQAYECWQQGADPIEFAKEHKEFARAFESFPGDADTIFPGWREKLGVHK [uniref90|Q8RTI1 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II n=1 Tax=magnetite-containing magnetic vibrio RepID=Q8RTI1_9PROT]
Q0F2Z8  : MDQSNRYADLSLNEADLIAGGKHLLVAYKLIPAKGYGFLEVAAHIAAESSTGTNVEVSTTDDFTRGVDALVYDIDETAFGDEGVTGGGLMKVAYPVELFDPNLIDGHYNVSHMWSLILGNNQGMGDHEGLRMLDFMVPECMIRKFDGPSAGIADLWKVLGRPEVDGGYISGTIIKPKLGLRPEPFAKACLDFWLGGDFIKNDEPQANQPFCPMKVVIPKVAEAMDRAQQETGQAKLFSANATADYHGECVARGEYILSEFAKYGNEKHVAFLIDGFVTGPAGVTTARRAFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLARLQGASGIHTGTMGYGKMEGHGKETVLAYMLERDECMGHYFNQKWYGMKPTAPIISGGMNALRLPGFFENLGHGNVINTCGGGSFGHIDSPAAGGKSLDQAYDCWKSGTDPIEYAKTHGEFARAFESFPGDADKLYPGWRDKLGVHK [uniref90|Q0F2Z8 Ribulose-bisphosphate carboxylase n=1 Tax=Mariprofundus ferrooxydans PV-1 RepID=Q0F2Z8_9PROT]
SecStr  : CCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCEEECCCCCCHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCEEEECCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEECCCCCCHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCHHCCCCCCCEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHHHHCCCC [Secondary structure predicted by PsiPred]
Target  : MDQSNRYANLNLKEEDLIKNGKHLLVAYKLIPAKGHGFLEVAAHVAAESSTGTNVEVSTTDDFTRGVDALVYEIDETAFGDDPVKGGGLFKVAYPVELFDPNLTDGTYNISHMWSLILGNNQGMGDHQGLRMLDFLVPEMMVRKFDGPSANISNLWKVLGRSETDGGYIAGTIIKPKLGLRPEPFAKACYDFWLGGDFIKNDEPQANQPFCPMEVVMPKVAEAMDRAQQATGQAKLFSANITADYYKEMIHRGDFVLETFAKYNSASHVAFLVDGFVTGPAGVTTARREFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLVRLMGASGMHTGTMGYGKMEGHGKETVLAYMLERDECQGPYFYQKWYGMKATTPIISGGMNALRLPGFFQNLGHGNVINTCGGGAFGHIDSPAAGGISLGQAYDCWKSGSDPIEYAKTHKEFARAFESFPKDGDKLFAGWREKLGVHK
Match   :   QSNRYA:L:LKEEDLIK:G:H|LVAY | PA G G|LE:AAH|AAESSTG            |GVDALVY IDE:          G|:KVAYP |LFD N:TDG   I  : :L |GNNQGMGD  :L:M DF VP  M:: FDGP: :IS:LW||LGR   DGGYI:GTIIKPKLGLRPEPFAKA:Y:FWLGGDFI:NDEPQ:NQ FCP:: V|P V |:| RAQ: TGQAKLFS NITAD | EM  R:DF:LETF:   :A: VAFLVDGFV GP: VTTARR||P: |LH|HRAGHG VTS :S  G   :   K| RL:GASG:H:GTMGYGKMEG   | ||AYM|ERD:C GP|||Q:WYGMK TTPIISGGMNALRLPGFF|NLGHGNVINT:GGG:|GHIDSPAAG:|SL QAY|CWK:G         HKEFARAFESFPKD:DKLF GWREKLGVHK
Template: ..QSNRYADLSLKEEDLIKGGNHILVAYTMEPAAGVGYLEAAAHIAAESSTG............KGVDALVYFIDEA.........KGIMKVAYPNDLFDRNVTDGRVMIVSFLTLCIGNNQGMGDIANLQMQDFYVPPRMLQLFDGPAKDISDLWRILGRPVKDGGYISGTIIKPKLGLRPEPFAKAAYQFWLGGDFIXNDEPQGNQVFCPIKKVLPLVYDSLKRAQDETGQAKLFSMNITADDHYEMCARADFALETFG...DADKVAFLVDGFVGGPGMVTTARRQYPSQYLHYHRAGHGMVTSPSSKRGYTAFVLAKMSRLQGASGIHVGTMGYGKMEGGKDDRIIAYMIERDSCTGPFYHQEWYGMKPTTPIISGGMNALRLPGFFENLGHGNVINTAGGGSYGHIDSPAAGAVSLRQAYECWKAG..DPIEWA.HKEFARAFESFPKDADKLFPGWREKLGVHK
SecStr  : ..HHHHHCTTTTHHHHHHHHCCCEEEEEEEECTTTTHHHHHHHHHHHHHCCC............GGCCCEEEEEECC.........CEEEEEEETTTTCCCCCCCCCCHHHHHHHHHHGGGGCTTTTEEEEEEEEECHHHHHHCCCCCCCCHHHHHHHHHCCCCCCCCEEEECCCCCCCCHHHHHHHHHHHHHHCCEEEEETTTTCCTTTTHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCHHHHHHHHHHHHHHHHH...TTTEEEEEEHHHHHCHHHHHHHHHHHCCCEEEEETTTTCCCCTTTTCCCCHHHHHHHHHHHHHCEEEEECTTTTCCCCCTTTTHHHHHHHHCEEEECCCEEEEETTTCCCEEEECCCCCCCHHHHHHHHHHCCCEEEEEHHHHHHCCCHHHHHHHHHHHHHHHHHHC..HHHHHH.HHHHHHHHHHCHHHHHHHHCHHHHHHHCCC [Secondary structure assigned by YASARA]
1RSC-G  : ....LTYYTPDYTP.....KDTDLLAAFRFSPQPGVPADEAGAAIAAESST.............DRYKGKCYHIEP............FAFIAYPLDLFEE.......SVTNILTSIVGNVFGFKAIRSLRLEDIRFPVALVKTFQGPPHGIQVERDLLNKY....RPMLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKSQAETGEIKGHYLNVTAPTCEEMMKRAEFAKEL..........IIMHDFLTAGFTANTTLAKWCRGVLLHIHRAMHAVIDR...NHGIHFRVLAKCLRLSGGDHLH..............TLGFVDLMREDHIEA.FFTQDWASMPGVLPVASGGIHVWHMPALVEIF.GDDSVLQFGGGTLGHPWGNAPGATANRVALEACVQ....LREAG.SPELAAALDLW................... [: RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (LARGE]
1GEH-B  : ..........GYEP.......RDIIAVFRVTPAEGYTIEQAAGAVAAESST.............ADLSAKAYDFHD............IVRIAYPFHAFEE.......NLPGLLASIAGNIFGMKRVKGLRLEDLYFPEKLIREFDGPAFGIEGVRKMLEIK....RPIYGVVPKPKVGYSPEEFEKLAYDLLSNADYMKDDENLTSPWYNRFEERAEIMAKIIDKVENETGEKKTWFANITAD.LLEMEQRLEVLADL..........HAMVDVVITGWGALRYIRDLAAGLAIHGHRAMHAAFTR...YHGISMFVLAKLYRLIGIDQLH..............VIQNARILRESHYK...LEQKFYSIKAAFPTSSGGLHPGNIQPVIEAL.GTDIVLQLGGGTLGHPDGPAAGARAVRQAIDAIMQG..PLDEYA.HKELARALEKW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE]
1SVD-A  : .....TYWMPEYTP.....LDSDILACFKITPQPGVDREEAAAAVAAESSTG............DYYKGRAYRIED............YAFIAYPIDLFEE.......SVVNVFTSLVGNVFGFKAVRGLRLEDVRFPLAYVKTCGGPPHGIQVERDKMNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFMRWRDRFLFVQDATETAEAQTGERKGHYLNVTAPTPEEMYKRAEFAKEI..........IIMHDYITGGFTANTGLAKWCQGVLLHIHRAMHAVIDR...NHGIHFRVLTKILRLSGGDHLH..............TLGWIDLLRESFIP..FFDQDWGSMPGVFAVASGGIHVWHMPALVNIF.GDDSVLQFGGGTLGHPWGNAAGAAANRVALEACVE....LTAAA.SPELKIAMETW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE]
2YBV-A  : ......YYTPDYTP.....KDTDILAAFRVTPQPGVPFEEAAAAVAAESSTG............DRYKGCCYDIEP............IAYIAYPLDLFEE.......SVTNMLTSIVGNVFGFKALKALRLEDLRIPVAYLKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKAQAETGEIKGHYLNVTAPTCEEMLKRAEFAKEL..........IIMHDFLTAGFTANTTLSKWCRGMLLHIHRAMHAVMDR...NHGIHFRVLAKCLRMSGGDHIH..............TLGFVDLLRENYIE..YFTQDWASMPGVMAVASGGIHVWHMPALVDIF.GDDAVLQFG.....HPWGNAPGATANRVALEACIQ....IREAA.SPELAAAC...................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN]
1BXN-C  : ....MGYWDGDYVP.....KDTDLLALFRITPQDGVDPVEAAAAVAGESST.............DMYRAKAYRVDP............FCYVAYDLSLFEE.......SIANLTASIIGNVFSFKPIKAARLEDMRFPVAYVKTFAGPSTGIIVERERLDKF....RPLLGATTKPKLGLSGRNYGRVVYEGLKGLDFMKDDENINSQPFMHWRDRFLFVMDAVNKASAATGEVKGSYLNVTAGTMEEMYRRAEFAKSL..........IIMVD.LIVGWTCIQSMSNWCRDMILHLHRAGHGTYTR...NHGVSFRVIAKWLRLAGVDHMH..............VQGYYNVCRDAYTQ..FFDQDWASLRKVMPVASGGIHAGQMHQLIHLF.GDDVVLQFGGGTIGHPQGIQAGATANRVALEAMVL....LRDAA.CGPLRAALDTW................... [: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)]
1EJ7-L  : .....TYYTPEYQT.....KDTDILAAFRVTPQPGVPPEEAGAAVAAESSTG............DRYKGRCYRIER............IAYVAYPLDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENVNSQPFMRWRDRFLFCAEALYKAQAETGEIKGHYLNATAGTCEEMIKRAVFAREL..........IVMHDYLTGGFTANTSLAHYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHIH..............TLGFVDLLRDDFVE..YFTQDWVSLPGVLPVASGGIHVWHMPALTEIF.GDDSVLQFGGGTLGHPWGNAPGAVANRVALEACVK....IREAC.SPELAAACEVW................... [: RUBISCO (LARGE SUBUNIT)]
1IWA-C  : ....MGYWNPDYQV.....KDTDVLALFRVTPQPGVDPIEAAAAVAGESST.............DLYRAKAYKVDQ............FAYIAYELDLFEE.......SIANLTASIIGNVFGFKAVKALRLEDMRLPLAYLKTFQGPATGVILERERLDKF....RPLLGCTTKPKLGLSGKNYGRVVYEALKGLDFVKDDENINSQPFMRWRERYLFTMEAVNKASAATGEVKGHYLNVTAATMEEMYARANFAKEL..........IIMID.LVIGYTAIQTMAKWARDMILHLHRAGNSTYSR...NHGMNFRVICKWMRMAGVDHIH..............TRGFYKTLLLPKLE..FFDMEWASLRKVMPVASGGIHAGQMHQLIHYLG.EDVVLQFGGGTIGHPDGIQAGATANRVALEAMIL....LREAA.CGALRTALDLW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE]
1TEL-B  : .....GFFAS...........QYLVLDYYLESV..GDIETALAHFCSEQSTA............RVHAAKVIDYEV............RVTIAHPHCNFGP.......KIPNLLTAVCGETYFTPGVPVVKLMDIHFPDTYLADFEGPKFGIEGLRDILNAH....RPIFFGVVKPNIGLSPGEFAEIAYQSWLGLDIAKDDEMLADVTWSSIEERAAHLGKARRKAEAETGEPKIYLANITDE.VDSLMEKHDVAVRN..........ALLINALPVGLSAVRMLSNYT.QVPLIGHFPFIASFSR...KYGIHSKVMTKLQRLAGLDAVI..............VLENVIECTKP..........MGRIKPCLPVPGGSDSALTLQTVYEKVGNVDFGFVPGRGVFGHPMGPKAGAKSIRQAWEAIEQG..SIETWA.HPELQAMVDQ.................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE, LARGE SUBUNIT]
2D69-A  : .....DFVDLNYEP.....GRDELIVEYYFEPN.GVSPEEAAGRIASESSIG............KRSMAKVFYLEK............IAKIAYPLTLFEE.......SLVQLFSAVAGNVFGMKALKNLRLLDFHPPYEYLRHFKGPQFGVQGIREFMGVK....RPLTATVPKPKMGWSVEEYAEIAYELWSGIDLLKDDENFTSFPFNRFEERVRKLYRVRDRVEAETGETKEYLINITGP.VNIMEKRAEMVANE..........YVMIDIVVAGWSALQYMREVTEGLAIHAHRAMHAAFTR...RHGITMLALAKAARMIGVDQIH..............IKRINDFLLS...........WEHIRPVFPVASGGLHPGLMPELIRLF.GKDLVIQAGGGVMGHPDGPRAGAKALRDAIDAAIEG..DLDEKA.SPELKKSLREV................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE]
2QYG-D  : .....GFYAK...........NYIELDFDFECA..GDPHEAAAHLCSEQSTA............PRFAAKVLELSA............RVTIAHPHGNF........AKIPNLLSAVCGEVFFSPGIPLIRLQDIRFPEPYLAAFDGPRFGIAGVRERLQAF....RPIFFGVIKPNIGLPPQPFAELGYQSWTGLDIAKDDEMLADVDWCPLAERAALLGDACRRASAETGVPKIYLANITDE.VDRLTELHDVAVAN..........ALLINAMPVGLSAVRMLRKHA.TVPLIAHFPFIAAFSR...NYGIHSRVMTRLQRLAGFDVVI..............VLDCIRACLE...........MGPIKPCLPVPGGSDSAATLENVYRKVGSADFGFVPGRGVFGHPMGPAAGATSIRQAWDAIAAG..PVPDHA.HPELAAALRAF................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE-LIKE PROTEIN 2]
2V67-A  : ....LTYYTPDYVV......DTDILAAFRMTPQPGVPPEECGAAVAAESST.............DRYKGRCYDIEP............IAYVAYXIDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFVGXPHGIQVERDKLNKY....RGLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTXDDENVNSQPFMRWRDRFLFVAEAIYKAQAETGEVKGHYLNATAGTCEEMMKRAVXAKEL..........IIMHDYLTGGFTANTSLAIYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHLH..............ILGFVDLMRDDYVE..YFTQDWXSMPGVMPVASGGIHVWHMPALVEIF.GDDACLQFGGGTLGHPWGNAPGAAANRVALEACTQ....IRSAC.SPELAAACEVW................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN]
3NWR-A  : ....................EDTLEADYLIET..PLDPARVADVMAGEQSSG............ARSRASVLRIEE............RITLSFPLANI.........NLPTLAATVAGNLYDLGEVTGVRLLSLRLPASYRARFELPRHGVAGTRALTDVK....RPMIGTIIKPNVGLSAAETAALVRELCEAVDFIXDDEVCANPAHAPLAERVRAVMSEVRRYRERSGRPVMVAFNITDD.LDAMRRHAELVERE..........CVMASINWCGFSAIQSLRRTT.PLVLHAHRNGYGMMSR...ALGMSFQAYQTLWRLSGVDHMH..............VIESARDCATP...............AVLPAFSSGQWAGTVQATFDAVRSTDLLFMSGGGILAHPDGPAAGVTSVRQAWAAVQAG..PLPVYA.MPELRRALAFF................... [: A RUBISCO-LIKE PROTEIN]
3QFW-B  : ......................RIVATYHIAS.....IEQRALALAIEQSVE.............NIVGRVEDVAE............AVRIGLAAATAP.......AEPGQLLNMLFGNSSIQPD...IALADVELPAHYLTAFGGPRVGLAGIRTLTGAQ....RALTASALKP.QGLSPAALASIAHQLALGVDLIKDDHGLADQAFSPFAERAAAVGKAVREANAARGGRTLYAPNISG.TLDDMRRQLGVIRDE..........AVLVAPMIVGVSNFHAIVKEAAGLVVVAHPAMAGAA........IAAPLLGRLFRLFGADATV..............CLALAQAARD...........FGKLNACIPTPAGGIMLQRVNELLRFYG.QDVMLLI..........LTEQASRFVNKVADYGQR....................................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE]
uniref90: ......................RIIATYRVTS.....IADRAQGLAIEQSVE.............GIVGRVALIDQ............AVRVALAAATAP.......AEPGQLLNMLFGNASIQPD...VALVDVELPPAYLAAFGGPKLGLDGIRARTGVH....RALTASALKP.QGLAPAALAAIARQLAEGVDLIKDDHGLADQAYSPFAARIAAVGRAVDAANQASGRRALYAPHVSG.SLDEMRRQLDLIRAE..........ALMMMPMIVGLSNFHVIAREAEGLVVLAHPALSGAT........IAPPLLGKLFRLLGADATV..............CRALADAARG...........WGGLKPCLPVPAGGIAIDRVEELLSFYG.RDVMLLI..........LGAEAARFVAEVAAHG......................................... [uniref90|Q2IV37 Ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit n=1 Tax=Rhodopseudomonas palustris HaA2 RepID=Q2IV37_RHOP2]
2ZVI-A  : ......................ELLATYLLT.....DTEKKAEQIATGLTVG............QKHKGRVIKVEE............VITIAYPEINFSQ.......DIPALLTTVFGKLSL...DGKIKLIDLHFSEAFKRALPGPKFGVYGIRKLLGE.....RPLLMSIFKGVIGRDLSDIKEQLRQQALGVDLIKDDEIFFETGLAPFETRIAEGKQILKETYEQTGHKTLYAVNLTGR.TADLKDKARRAAEL..........ALLFNVFAYGLDVMQGLAED..PVPIMAHPAVSGAFTS...FYGFSHALLGKLNRYCGADFSL..............ALAIHEECVR.............AFNQTFAVPSAGIHPGMVPLLMRDF.GIDHIINAGGGVHGHPNGAQGGGRAFRAIIDAVLEA..PIDEKA.CKDLKLALDKWGK................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE]
uniref90: ......................ELLATYILA.....DAEKRAEQIAIGLTVG............KKHKGRVVNVEE............TVTIAYPEANFTN.......DIPAVLTTVFGKLSL...DGKIKLADLEFSRSFKQSLPGPKFGVYGIRKKIGE.....RPLLMSIFKGVIGRDMEDLKEQLRQQALGVDLIKDDEILFETGSAPFEKRITEGKKVLEEAFEETGRKTLYAVNLTGR.TMELKAKARKAAEL..........VLLLNVFAYGLDVLQSFAED..PLPIMAHPAVSGALTS...HYGFSHSLLGKLNRYAGADFSL..............ALAIYDECTK.............VFKPTFAVPSAGIHPGMVPLLMKDF.GIDHIINAGGGIHGHPNGAAGGGRAFRAVIDAVLEA..PVEEKA.SPDLKLALEKWGR................. [uniref90|Q65KJ8 2,3-diketo-5-methylthiopentyl-1-phosphate enolase n=2 Tax=Bacillus RepID=MTNW_BACLD]
2OEK-B  : ......................AVMATYLLHDE..TDIRKKAEGIALGLTIG............RKHKGEVVAIEE............IVKIAYPTVNFSA.......DLPALLVTTFGKLSLD...GEVRLLDLEFPDEWKRQFPGPRFGIDGIRDRVGVH....RPLLMSIFKGMIGRDLAYLTSELKKQALGVDLVXDDEILFDSELLPFEKRITEGKAALQEVYEQTGKRTLYAVNLTGK.TFALKDKAKRAAEL..........VLLFNVFAYGLDVLQALRED..AVPIMAHPAFSGAVTP...FYGVAPSLWGKLLRLAGADFVL..............ALGIARALTD.............PFARAFPVPSAGIHPGLVPLIIRDF.GLDTIVNAGGGIHGHPDGAIGGGRAFRAAIDAVLAG..PLRAAA.NEALQKAIDRWGV................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE ENOLASE]
uniref90: .......................ILVTYLTQAK...DLNKKAQAIAVGMTVG............APYLGEAVSATP............LITVSYPTRNFTA.......DIPSLLTGIFGKLSMD...GKIKLVDIVFPESFLQAFPGPKFGIDGLRERLGAH....RPLLMSIFKSCLGLPFDDLKTQFRAQALGVDLVKDDEIFFADDRAPFIERIKAFKQIAQETEAETGKPVLYAANLTGP.VHELNEKAKRAVEA..........CLLFNVLAFGFDALHRLAAD..HVPIMAHPALAGAYYP...DYGIATPLLGTLMRVAGADLVL..............ALQLAKHLTD.............GVRRSFPVPSAGIHPGLVPQLYQDF.GLDQIVNAGGGIHGHPGGATAGAKAFVAAIEAVTAG..TLEEAS.SQELAIALEKWG.................. [uniref90|C0ZL40 2,3-diketo-5-methylthiopentyl-1-phosphate enolase n=1 Tax=Brevibacillus brevis NBRC 100599 RepID=C0ZL40_BREBN]
3FK4-A  : ......................GIIATYLIHDD...NLEKKAEQIALGLTIG............KQHKGNVIHVEE............IIKIEYPLLNFSP.......DLPAILTTTFGKLSLD...GEVKLIDLTFSDELKKHFPGPKFGIDGIRNLLQVH....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENALTPLTKRIVSGKEVLQSVYETYGHKTLYAVNLTGR.TFDLKENAKRAVQA..........ILLFNVFAYGLDVLQSLAED..PVPIMAHPAVSGAYSA...LYGVSSPLLGKLLRYAGADFSL..............ALAISKYLTE...........DASFKKSFSVPSAGIHPGFVPFIVRDF.GKDVVINAGGGIHGHPNGAQGGGKAFRTAIDATLQN..PLHEV..DINLHSALQIWG.................. [: RUBISCO-LIKE PROTEIN]
uniref90: ......................GIIATYLIHDD...NLEKKAEQIALGLTIG............KQHKGNVLHVEE............IIKIEYPLLNFSP.......DLPAILTTTFGKLSLD...GEVKLIDLTFSDELKKHFPGPKFGIDGIRNLLQVH....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENALTPLTNRIVSGKEVLQSVYETYGHKTLYAVNVTGR.TFDLKENAKRAVQA..........ILLFNVFAYGLDVLQSLAED..PVPIMAHPAVSGAYSA...LYGISSPLLGKLLRYAGADFSL..............ALAISKYLTE...........DVFFKKSFSVPSAGIHPGFVPFIIRDF.GKDVVINAGGGIHGHPNGAQGGGKAFRTAIDATLQN..PLHEV..DINLHSALQIWG.................. [uniref90|C3P745 2,3-diketo-5-methylthiopentyl-1-phosphate enolase n=71 Tax=Bacillus cereus group RepID=MTNW_BACAA]

NOTE: To save space, only 20 of 1107 template profile alignments are shown above. The complete set of alignments can be found in the file Homology_5c2c-~_profile.ali. The template profile contains structural alignments of 16 PDB files, which provide safe anchors for the remaining sequence-based alignments (only reliable regions shown).

In the alignment above, 441 of 470 target residues (93.8%) are aligned to template residues. Among these aligned residues, the sequence identity is 68.0% and the sequence similarity is 78.9% ('similar' means that the BLOSUM62 score is > 0). The following 6 loops had to be modeled (only the first of 2 similar loops in the homodimer is listed):

LoopN-terminal anchorLoop sequenceC-terminal anchor
1DPIEYAKTHKEFA
3DCWKSGSDPIEYA
5LETFAKYNSASHV
7EIDETAFGDDPVKGGGLFK
9ESSTGTNVEVSTTDDFTRGVDA
11NoneMDQSNRY

After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).

The resulting half-refined model has been saved as Homology_5c2c-~02_refined050.yob and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals0.156Optimal
Packing 1D-1.010Satisfactory
Packing 3D-1.193Satisfactory
Overall-0.926Good

Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as Homology_5c2c-~02_refined100.yob, the corresponding Z-scores are listed below:

Check typeQuality Z-scoreComment
Dihedrals0.451Optimal
Packing 1D-0.587Good
Packing 3D-1.384Satisfactory
Overall-0.807Good

Since the overall quality Z-score improved to -0.807 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.

NOTE: 4 residues contained in N- and C-terminal unaligned tails of the homodimeric model have been excluded from the Z-scores in both tables above, since they are not reliable (YASARA does not yet perform ab initio structure prediction) and would have mainly added noise to the result.

The final model for this template and alignment has been saved as Homology_5c2c-~02.yob, and is shown below, together with a plot of its overall quality Z-score, shown per residue:

6.5. Homology model 5/15, based on template 5HQM-~, alignment variant 01

This model is a homodimer, and based on the following profile-profile alignment:

(To improve readability, only up to ten lines of the complete target multiple sequence alignment (MSA) shown above are also displayed here (upside down). The template MSA has been shrunk and focused on structurally aligned PDB entries. The actual target-template alignment can be found in the middle at the line named 'Match'.)

Q08EW6  : .......................................................................................................................NNQGGGDIEHAKIHGIYMPERAIQLFDGPSKDISDMWRILGRPVKDGGYNAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEIQGNQVFSPMNQTIPLVVDAMKRAQDETGQAKLFSANITADDQYEMCARADFILEAFGP..DADKVAFLVDGYVGDPGMITTARSQYPNQYLHYHRAGHGAVNSPKIKRGYTAFVLAKMSRLQGASGAHVGTMGYGKME................................................................................................................................ [uniref90|Q08EW6 Ribulose 1,5-bisphosphate carboxylase/oxygenase large subunit (Fragment) n=1 Tax=uncultured marine bacterium RepID=Q08EW6_9BACT]
Q5DVV5  : ............................................................................................................................................................................IIKPKLGLRPKPFAEACYNFWLGGDFIKNDEPQGNQIWGPIKEVVPLVKDSLVRAQDDTGMAKLFSFNITADDHYEMLHRGEYILETFAEFSE..NIAFLVDGCVGGPGMVTTARRNFPDQFLHYHRAGHGAVTSDQSDRGYNMLVHMKMARLQGASGIHTGTMGYGKMEGAADDKVIAYMLERDSADGLSYHQEWEGMKATTPIICGGMNA...................................................................................... [uniref90|Q5DVV5 Ribulose-1,5-bisphosphate carboxylase oxygenase large subunit (Fragment) n=11 Tax=uncultured prokaryote RepID=Q5DVV5_9ZZZZ]
Q933G7  : ........................................................................................................................................VPPAYLRLFDGPSTTIKDLWRVLGRPVVDGGFIVGTIIKPKLGLRPQPFADACYDFWLGGDFIKNDEPQGNQVFAPFKDTVRAVNDAMRRAQDATGQPKLFSFNITADDHYEMLARGEYILETFGE..NADHVAFLVDGYVAGPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHVGTMGYGKMEGEASDRDSAFMITQDSAEGPYFKQEW...................................................................................................... [uniref90|Q933G7 Form II ribulose 1,5-bisphosphate carboxylase/oxygenase (Fragment) n=5 Tax=Rhodopseudomonas palustris RepID=Q933G7_RHOPA]
F2ZCE9  : .....................................................................................................................................DFYVPPDFLRLFDGPATTISNLWRVLGRPHQNGGFIVGTIVKPKLGLRPRPFADACYDFWLGGDFIKNDEPQGNQTFSPLKETIPLVADAMRRAQDETGEAKLFSANITADDHYEMVARGEFILDTFGEF..ADHVAFLVDGYVAGAAAVTTARRSFPQQYLHYHRAGHGAITSPQSKRGYTAFVHCKMARLQGASGIHTGTMSFGKMEGEAADRAIAFMLEQDSADGPYFHQEWHGMNPTTSIISG.......................................................................................... [uniref90|F2ZCE9 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=1 Tax=uncultured bacterium RepID=F2ZCE9_9BACT]
F2ZCD0  : ......................................................................................................................GNNQGMGDIANAQMQDFYVPPAMLALFDGPAKSINDLWTLLGRDNENGGYIAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEPQGNQVFCPLKKVLPLVHDAMKRAQDETGEAKLFSLNITADDHYEMCARADFGLETFGE..DAPRLAFLVDGFVGGPGMVTTARRQYSSQYLHYHRAGHGMITSPSSKRGYTAYILAKMSRLMGASGIHVGTMGYGKMEGGADDKIIAYMIERDECQGPFYYQKWHGMKPTTPIVSGGM........................................................................................ [uniref90|F2ZCD0 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=4 Tax=uncultured bacterium RepID=F2ZCD0_9BACT]
F5BZE6  : ......................................................................................................................GNNQGMGDVEYAKMIDFYMARSLLTLFDGPAMNITDMWRVLGRPQVNGGMVVGTIIKPKLGLRPKPFADACYMFWMGGDFIKNDEPQGNQVFAPTREIIPLVAEAMERAQQETGEAKIFSANITADDPFEMIRRGEFILEAFGK..NASHVAFLVDGYVGGPSAVTLCRRYFPNQFLHYHRAGHGAVTSNQSKRGYTVLTHMKMSRLQGASGIHTGTMGYGKMEGDKNEKMVAYMIERDEAMGVYYNQPWHGMTATTPIISGGMNALR.................................................................................... [uniref90|F5BZE6 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II (Fragment) n=1 Tax=alpha proteobacterium LM-5 RepID=F5BZE6_9PROT]
Q9FPW1  : LDQSSRYADLSLDEATLVKNGKHVLVAYIMKPKAGYDYLATAAHFAAESSTGTNVNVCTTDDFTKSVDALVYYIDPDSEE.........MKIAYPTLLFDRNIIDGRGMMCSFLTLAIGNNQGMGDVEYGKIYDFYLPPSFLRLYDGPAVNVEDMWRILGKGTSNGGLVDGTIIKPKLGLQPNPFGEACYSFWQGGDFIKNDEPQGNQVFCQMNECIPEVVKAMRACVKETGSSKLFSANITADDPEEMIARGKYIMSQFGPLSE..NCAFLVDGYVAGGTAVTCCRRNFPKQFLHYHRAGHGSVTSPQTQRGYTAFVHTKISRVIGASGIHVGTMSFGKMEGDASDKNIAYMLQDDEADGPYYRQEWQGMKETTPIISGGMNALRLPAFFENLGHSNVILTAGGGSFGHKDGPKIGAISCRQGEEAWKSLSDVIEYAKTHEEIKGAFLTFQKDADQIYPGWKEKLG... [uniref90|Q9FPW1 Ribulose 1,5-bisphosphate carboxylase oxygenase large subunit n=1 Tax=Symbiodinium sp. RepID=Q9FPW1_SYMSP]
E6VVI6  : .DQTSRYVNFDLKEDQLIADGNHVLCAYIYKPANGYGNVEVAAHFAAESSTGTNVEVCTTDDFTKGVDALVYEVSDASNGDS......LMKIAYPVELFDRNIIDGRAMLASFLTLCIGNNQGMGDVAYAKMHDFYVPRQYLELFDGPSKNIADFWRMLGRPTENGGMIAGTIVKPKLGLRPKPFADACYHFWLGGDFVKNDEPQGNQVFAPLKETITAVADAMRRAQDETGEAKIFSANITADDPREMIARGEFILNAFGE..NASRVAFLVDGYVAGPTAITTARRNFPNQFLHYHRAGHGAVTSPQAKRGYTAFVLSKMSRLQGASGIHTGTMGFGKMEGEMADKSMAYMIEREEAQGPYFKQKWYGMKATTPMISGGMNALRLPGFFDNLGHSNICQTSGGGAFGHLDGPTAGALSLRQSHDAWIQGVNLLDYAKEHNELARAFESFPGDADRFYPTWRHQL.... [uniref90|E6VVI6 Ribulose-bisphosphate carboxylase n=1 Tax=Desulfovibrio aespoeensis Aspo-2 RepID=E6VVI6_DESAO]
Q8RTI1  : MDQSNRYADLSLKEDDLIKGGNHVLVAYLMKPKTGYGYLEAAAHFSAESSTGTNVEVSTTDDFTKGVDALVYEIDEAK.........EIMKIAYPVDLFDRNITDGRAMIVSFLTLAIGNNQGMGDIAYAKMLDFYVPQKYLRLFDGPSKDISDLWRILGRPVVNGGYIAGTIIKPKLGLRPKPFAEAAYQFWLGGDFIKNDEPQGNQVFSPMRETIPLVYDSMKRAMDETGEAKLFSANITADDHYEMMARGEFILNTFGP..DADKVAFLVDGYVGGPGMVTTARRHFANQYLHYHRAGHGAVTSPSAKRGYTAFVLAKMSRLQGASGIHVGTMGYGKMEGDATDKNIAYMIERDSADGPFYHQEWYGMKPTTPIISGGMNALRLPGFFENLGHANLINTSGGGSYGHIDSPAAGAISLRQAYECWQQGADPIEFAKEHKEFARAFESFPGDADTIFPGWREKLGVHK [uniref90|Q8RTI1 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II n=1 Tax=magnetite-containing magnetic vibrio RepID=Q8RTI1_9PROT]
Q0F2Z8  : MDQSNRYADLSLNEADLIAGGKHLLVAYKLIPAKGYGFLEVAAHIAAESSTGTNVEVSTTDDFTRGVDALVYDIDETAFGDEGVTGGGLMKVAYPVELFDPNLIDGHYNVSHMWSLILGNNQGMGDHEGLRMLDFMVPECMIRKFDGPSAGIADLWKVLGRPEVDGGYISGTIIKPKLGLRPEPFAKACLDFWLGGDFIKNDEPQANQPFCPMKVVIPKVAEAMDRAQQETGQAKLFSANATADYHGECVARGEYILSEFAKYGNEKHVAFLIDGFVTGPAGVTTARRAFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLARLQGASGIHTGTMGYGKMEGHGKETVLAYMLERDECMGHYFNQKWYGMKPTAPIISGGMNALRLPGFFENLGHGNVINTCGGGSFGHIDSPAAGGKSLDQAYDCWKSGTDPIEYAKTHGEFARAFESFPGDADKLYPGWRDKLGVHK [uniref90|Q0F2Z8 Ribulose-bisphosphate carboxylase n=1 Tax=Mariprofundus ferrooxydans PV-1 RepID=Q0F2Z8_9PROT]
SecStr  : CCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCEEECCCCCCHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCEEEECCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEECCCCCCHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCHHCCCCCCCEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHHHHCCCC [Secondary structure predicted by PsiPred]
Target  : MDQSNRYANLNLKEEDLIKNGKHLLVAYKLIPAKGHGFLEVAAHVAAESSTGTNVEVSTTDDFTRGVDALVYEIDETAFGDDPVKGGGLFKVAYPVELFDPNLTDGTYNISHMWSLILGNNQGMGDHQGLRMLDFLVPEMMVRKFDGPSANISNLWKVLGRSETDGGYIAGTIIKPKLGLRPEPFAKACYDFWLGGDFIKNDEPQANQPFCPMEVVMPKVAEAMDRAQQATGQAKLFSANITADYYKEMIHRGDFVLETFAKYNSASHVAFLVDGFVTGPAGVTTARREFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLVRLMGASGMHTGTMGYGKMEGHGKETVLAYMLERDECQGPYFYQKWYGMKATTPIISGGMNALRLPGFFQNLGHGNVINTCGGGAFGHIDSPAAGGISLGQAYDCWKSGSDPIEYAKTHKEFARAFESFPKDGDKLFAGWREKLGVHK
Match   : MDQSNRYANLNLKE:|LI :G|H:L AY | P    :F||:AAH AAESSTGTNVEVSTTDDFTRGVDALVYE|DE:          :L:K|AYP|ELFD N: DG   I: : :L |GNNQGMGD |  |M DF VP   :| FDGPS::I::LW|VLGR   :GG|I:GTIIKPKLGLRP|PFA:ACYDFWLGGDFI:NDEPQ:NQ F:P:: ::  VA|AM RAQ: TG|AKLFS NITAD | EM| RG|F|LETFA   :A:H|AFLVDG|V:GPA:VTTARR FP  |LH|HRAGHGAVTS :S  G   :   K|:RL:GASG:HTGTMG|GKMEG:: | :|AYM| :D ::GPYF|Q:W GM: TTPIISGGMNALR|PGFF:NLGH:N:I T:GGGAFGH|D: AAG: SL QA :CWK:G:DP|E|AK H|EFARAFESFP:D:DKL| :WR KLGV: 
Template: MDQSNRYANLNLKESELIAGGRHVLCAYIMKPK...NFIQTAAHFAAESSTGTNVEVSTTDDFTRGVDALVYEVDEA..........SLMKIAYPIELFDRNVIDGRAMIASFLTLTIGNNQGMGDVEYAKMYDFYVPPAYLKLFDGPSTTIKDLWRVLGRPVINGGFIVGTIIKPKLGLRPQPFANACYDFWLGGDFIXNDEPQGNQVFAPFKDTVRAVADAMRRAQDKTGEAKLFSFNITADDHYEMLARGEFILETFAD..NADHIAFLVDGYVAGPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHTGTMGFGKMEGEAADRAIAYMITEDAADGPYFHQEWLGMNPTTPIISGGMNALRMPGFFDNLGHSNLIMTAGGGAFGHVDGGAAGAKSLRQAEQCWKQGADPVEFAKDHREFARAFESFPQDADKLYPNWRAKLGVED
SecStr  : CCCCCCEEETTTHHHHHHHHCCCEEEEEEEECT...HHHHHHHHHHHHHCCCCCCCTTTTHHHHHHCCCEEEEEETT..........EEEEEEETTTTCCCCCCCCCCCHHHHHHHHHGGGGCTTTTEEEEEEEEECTTTTTTTTCCCCCCHHHHHHHHHCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCEEEEETTTTCCTTTTHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCHHHHHHHHHHHHHHHHHC..TTTEEEEEEHHHHHCHHHHHHHHHHHCCCEEEEETTTTCCCCTTTTCCCCHHHHHHHHHHHHHCEEEEECTTTTCCCCCTTTTHHHHHHHHHEEEECCCEEEEETTTCCCEEEECCCCCCCHHHHHHHHHHCCCEEEEETTTTCCCCCHHHHHHHHHHHHHHHHHHCCHHHHHHCCHHHHHHHHHHCHHHHHHHHCHHHHHHCCCC [Secondary structure assigned by YASARA]
1RSC-G  : ....LTYYTPDYTP.....KDTDLLAAFRFSPQ....ADEAGAAIAAESST..........TDMDRYKGKCYHIEP............FAFIAYPLDLFEE.......SVTNILTSIVGNVFGFKAIRSLRLEDIRFPVALVKTFQGPPHGIQVERDLLNKY....RPMLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKSQAETGEIKGHYLNVTAPTCEEMMKRAEFAKEL..........IIMHDFLTAGFTANTTLAKWCRGVLLHIHRAMHAVIDR...NHGIHFRVLAKCLRLSGGDHLH..............TLGFVDLMREDHIEA.FFTQDWASMPGVLPVASGGIHVWHMPALVEIF.GDDSVLQFGGGTLGHPWGNAPGATANRVALEACVQ...LREAGKWSPELAAALDLW................... [: RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (LARGE]
1GEH-B  : ..........GYEP.......RDIIAVFRVTPA....IEQAAGAVAAESST.GTWT..YEQERWADLSAKAYDFHD............IVRIAYPFHAFEE.......NLPGLLASIAGNIFGMKRVKGLRLEDLYFPEKLIREFDGPAFGIEGVRKMLEIK....RPIYGVVPKPKVGYSPEEFEKLAYDLLSNADYMKDDENLTSPWYNRFEERAEIMAKIIDKVENETGEKKTWFANITAD.LLEMEQRLEVLADL..........HAMVDVVITGWGALRYIRDLAAGLAIHGHRAMHAAFTR...YHGISMFVLAKLYRLIGIDQLH..............VIQNARILRESHYK...LEQKFYSIKAAFPTSSGGLHPGNIQPVIEAL.GTDIVLQLGGGTLGHPDGPAAGARAVRQAIDAIMQGIPLDEYAKTHKELARALEKW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE]
1SVD-A  : .....TYWMPEYTP.....LDSDILACFKITPQ....REEAAAAVAAESSTG..........DMDYYKGRAYRIED............YAFIAYPIDLFEE.......SVVNVFTSLVGNVFGFKAVRGLRLEDVRFPLAYVKTCGGPPHGIQVERDKMNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFMRWRDRFLFVQDATETAEAQTGERKGHYLNVTAPTPEEMYKRAEFAKEI..........IIMHDYITGGFTANTGLAKWCQGVLLHIHRAMHAVIDR...NHGIHFRVLTKILRLSGGDHLH..............TLGWIDLLRESFIP..FFDQDWGSMPGVFAVASGGIHVWHMPALVNIF.GDDSVLQFGGGTLGHPWGNAAGAAANRVALEACVE...LTAAAQHSPELKIAMETW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE]
2YBV-A  : ......YYTPDYTP.....KDTDILAAFRVTPQ....FEEAAAAVAAESSTG........LTDLDRYKGCCYDIEP............IAYIAYPLDLFEE.......SVTNMLTSIVGNVFGFKALKALRLEDLRIPVAYLKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKAQAETGEIKGHYLNVTAPTCEEMLKRAEFAKEL..........IIMHDFLTAGFTANTTLSKWCRGMLLHIHRAMHAVMDR...NHGIHFRVLAKCLRMSGGDHIH..............TLGFVDLLRENYIE..YFTQDWASMPGVMAVASGGIHVWHMPALVDIF.GDDAVLQFG.....HPWGNAPGATANRVALEACIQ...IREAARWSPELAAAC...................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN]
1BXN-C  : ....MGYWDGDYVP.....KDTDLLALFRITPQ....PVEAAAAVAGESST..WTV......ACDMYRAKAYRVDP............FCYVAYDLSLFEE.......SIANLTASIIGNVFSFKPIKAARLEDMRFPVAYVKTFAGPSTGIIVERERLDKF....RPLLGATTKPKLGLSGRNYGRVVYEGLKGLDFMKDDENINSQPFMHWRDRFLFVMDAVNKASAATGEVKGSYLNVTAGTMEEMYRRAEFAKSL..........IIMVD.LIVGWTCIQSMSNWCRDMILHLHRAGHGTYTR...NHGVSFRVIAKWLRLAGVDHMH..............VQGYYNVCRDAYTQ..FFDQDWASLRKVMPVASGGIHAGQMHQLIHLF.GDDVVLQFGGGTIGHPQGIQAGATANRVALEAMVL...LRDAARWCGPLRAALDTW................... [: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)]
1EJ7-L  : .....TYYTPEYQT.....KDTDILAAFRVTPQ....PEEAGAAVAAESSTGTWTTV.....SLDRYKGRCYRIER............IAYVAYPLDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENVNSQPFMRWRDRFLFCAEALYKAQAETGEIKGHYLNATAGTCEEMIKRAVFAREL..........IVMHDYLTGGFTANTSLAHYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHIH..............TLGFVDLLRDDFVE..YFTQDWVSLPGVLPVASGGIHVWHMPALTEIF.GDDSVLQFGGGTLGHPWGNAPGAVANRVALEACVK...IREACKWSPELAAACEVW................... [: RUBISCO (LARGE SUBUNIT)]
1IWA-C  : ....MGYWNPDYQV.....KDTDVLALFRVTPQ....PIEAAAAVAGESST...........AADLYRAKAYKVDQ............FAYIAYELDLFEE.......SIANLTASIIGNVFGFKAVKALRLEDMRLPLAYLKTFQGPATGVILERERLDKF....RPLLGCTTKPKLGLSGKNYGRVVYEALKGLDFVKDDENINSQPFMRWRERYLFTMEAVNKASAATGEVKGHYLNVTAATMEEMYARANFAKEL..........IIMID.LVIGYTAIQTMAKWARDMILHLHRAGNSTYSR...NHGMNFRVICKWMRMAGVDHIH..............TRGFYKTLLLPKLE..FFDMEWASLRKVMPVASGGIHAGQMHQLIHYLG.EDVVLQFGGGTIGHPDGIQAGATANRVALEAMIL...LREAAKTCGALRTALDLW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE]
1TEL-B  : .....GFFAS...........QYLVLDYYLESV....IETALAHFCSEQSTA........DEDFRVHAAKVIDYEV............RVTIAHPHCNFGP.......KIPNLLTAVCGETYFTPGVPVVKLMDIHFPDTYLADFEGPKFGIEGLRDILNAH....RPIFFGVVKPNIGLSPGEFAEIAYQSWLGLDIAKDDEMLADVTWSSIEERAAHLGKARRKAEAETGEPKIYLANITDE.VDSLMEKHDVAVRN..........ALLINALPVGLSAVRMLSNYT.QVPLIGHFPFIASFSR...KYGIHSKVMTKLQRLAGLDAVI..............VLENVIECTKP..........MGRIKPCLPVPGGSDSALTLQTVYEKVGNVDFGFVPGRGVFGHPMGPKAGAKSIRQAWEAIEQGISIETWAETHPELQAMVDQ.................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE, LARGE SUBUNIT]
2D69-A  : .....DFVDLNYEP.....GRDELIVEYYFEPN....PEEAAGRIASESSIGTW.........AKRSMAKVFYLEK............IAKIAYPLTLFEE.......SLVQLFSAVAGNVFGMKALKNLRLLDFHPPYEYLRHFKGPQFGVQGIREFMGVK....RPLTATVPKPKMGWSVEEYAEIAYELWSGIDLLKDDENFTSFPFNRFEERVRKLYRVRDRVEAETGETKEYLINITGP.VNIMEKRAEMVANE..........YVMIDIVVAGWSALQYMREVTEGLAIHAHRAMHAAFTR...RHGITMLALAKAARMIGVDQIH..............IKRINDFLLS...........WEHIRPVFPVASGGLHPGLMPELIRLF.GKDLVIQAGGGVMGHPDGPRAGAKALRDAIDAAIEGVDLDEKAKSSPELKKSLREV................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE]
2QYG-D  : .....GFYAK...........NYIELDFDFECA....PHEAAAHLCSEQSTA...........RPRFAAKVLELSA............RVTIAHPHGNF........AKIPNLLSAVCGEVFFSPGIPLIRLQDIRFPEPYLAAFDGPRFGIAGVRERLQAF....RPIFFGVIKPNIGLPPQPFAELGYQSWTGLDIAKDDEMLADVDWCPLAERAALLGDACRRASAETGVPKIYLANITDE.VDRLTELHDVAVAN..........ALLINAMPVGLSAVRMLRKHA.TVPLIAHFPFIAAFSR...NYGIHSRVMTRLQRLAGFDVVI..............VLDCIRACLE...........MGPIKPCLPVPGGSDSAATLENVYRKVGSADFGFVPGRGVFGHPMGPAAGATSIRQAWDAIAAGIPVPDHAASHPELAAALRAF................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE-LIKE PROTEIN 2]
2V67-A  : ....LTYYTPDYVV......DTDILAAFRMTPQ....PEECGAAVAAESST...........SLDRYKGRCYDIEP............IAYVAYXIDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFVGXPHGIQVERDKLNKY....RGLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTXDDENVNSQPFMRWRDRFLFVAEAIYKAQAETGEVKGHYLNATAGTCEEMMKRAVXAKEL..........IIMHDYLTGGFTANTSLAIYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHLH..............ILGFVDLMRDDYVE..YFTQDWXSMPGVMPVASGGIHVWHMPALVEIF.GDDACLQFGGGTLGHPWGNAPGAAANRVALEACTQ...IRSACKWSPELAAACEVW................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN]
3NWR-A  : ....................EDTLEADYLIET.....PARVADVMAGEQSSG............ARSRASVLRIEE............RITLSFPLANI.........NLPTLAATVAGNLYDLGEVTGVRLLSLRLPASYRARFELPRHGVAGTRALTDVK....RPMIGTIIKPNVGLSAAETAALVRELCEAVDFIXDDEVCANPAHAPLAERVRAVMSEVRRYRERSGRPVMVAFNITDD.LDAMRRHAELVERE..........CVMASINWCGFSAIQSLRRTT.PLVLHAHRNGYGMMSR...ALGMSFQAYQTLWRLSGVDHMH..............VIESARDCATP...............AVLPAFSSGQWAGTVQATFDAVRSTDLLFMSGGGILAHPDGPAAGVTSVRQAWAAVQAGTPLPVYAEHMPELRRALAFF................... [: A RUBISCO-LIKE PROTEIN]
3QFW-B  : ......................RIVATYHIAS.....IEQRALALAIEQSVEC............NIVGRVEDVAE............AVRIGLAAATAP.......AEPGQLLNMLFGNSSIQPD...IALADVELPAHYLTAFGGPRVGLAGIRTLTGAQ....RALTASALKP.QGLSPAALASIAHQLALGVDLIKDDHGLADQAFSPFAERAAAVGKAVREANAARGGRTLYAPNISG.TLDDMRRQLGVIRDE..........AVLVAPMIVGVSNFHAIVKEAAGLVVVAHPAMAGAA........IAAPLLGRLFRLFGADATV..............CLALAQAARD...........FGKLNACIPTPAGGIMLQRVNELLRFYG.QDVMLLI..........LTEQASRFVNKVADYGQR....................................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE]
uniref90: ......................RIIATYHLAS.....VAERAKGLAIEQSVEC............TIVGRVEDIAE............AVRIGLAAATAP.......AEPGQLINMLFGNSSMQQD...VTLVDVELPPSYLAAFGGPRLGLAGLRALTGTQ....RALTASALKP.QGLSPAALARIAGQLARGVDVIKDDHGIADQAYSPFAARVEAVGRAVQEANVARDGHSLYAPNLSG.TLDDMRRQLDLAREQ..........AVMVAPMIVGLANFHAVVKAAAGMVVIAHPALSGVT........IAPPLLGKLFRLFGADATI..............CLQLARAGRD...........WGALEPCMPVPAGGLTADRVAELLQFYG.HDVMLLI..........LTEEAARFVNEVAAHGK........................................ [uniref90|Q07KC6 Ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit n=1 Tax=Rhodopseudomonas palustris BisA53 RepID=Q07KC6_RHOP5]
2ZVI-A  : ......................ELLATYLLT......TEKKAEQIATGLTVG...........MQKHKGRVIKVEE............VITIAYPEINFSQ.......DIPALLTTVFGKLSL...DGKIKLIDLHFSEAFKRALPGPKFGVYGIRKLLGE.....RPLLMSIFKGVIGRDLSDIKEQLRQQALGVDLIKDDEIFFETGLAPFETRIAEGKQILKETYEQTGHKTLYAVNLTGR.TADLKDKARRAAEL..........ALLFNVFAYGLDVMQGLAED..PVPIMAHPAVSGAFTS...FYGFSHALLGKLNRYCGADFSL..............ALAIHEECVR.............AFNQTFAVPSAGIHPGMVPLLMRDF.GIDHIINAGGGVHGHPNGAQGGGRAFRAIIDAVLEAQPIDEKAEQCKDLKLALDKWGK................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE]
uniref90: ......................ELLATYVLT......DERKAEQIALGLTVG...........LQKHKGRVEKVTE............EVTIAYPEANFSA.......DIPAVLSTIFGKLSL...DGKVKLVDIQFSDRFKKSLPGPVFGIDGIRKKTGV.....RPLLMSIFKGVIGRDMTDLKEQLRLQALGVDFIKDDEILFESPLAPFEDRIKEGKKILKETYEETGHRTLYAVHLTGR.TFELRDRARKAAEL..........ALLFNVFAYGLDVMQSLAED..RLPIMAHPAVSGALTS...EYGFSHSLLGKLNRYAGADLSL..............AFGIYEACVK.............SVQKTFPVPSAGIHPGMVPVLMKDF.GLDHVINAGGGIHGHPRGAIGGGKAFRSIIDAVIHGESIQEKTASCQDLKAALELWGR................. [uniref90|A8FCG8 2,3-diketo-5-methylthiopentyl-1-phosphate enolase n=2 Tax=Bacillus pumilus RepID=MTNW_BACP2]
2OEK-B  : ......................AVMATYLLHDE....IRKKAEGIALGLTIG...........LRKHKGEVVAIEE............IVKIAYPTVNFSA.......DLPALLVTTFGKLSLD...GEVRLLDLEFPDEWKRQFPGPRFGIDGIRDRVGVH....RPLLMSIFKGMIGRDLAYLTSELKKQALGVDLVXDDEILFDSELLPFEKRITEGKAALQEVYEQTGKRTLYAVNLTGK.TFALKDKAKRAAEL..........VLLFNVFAYGLDVLQALRED..AVPIMAHPAFSGAVTP...FYGVAPSLWGKLLRLAGADFVL..............ALGIARALTD.............PFARAFPVPSAGIHPGLVPLIIRDF.GLDTIVNAGGGIHGHPDGAIGGGRAFRAAIDAVLAGRPLRAAAAENEALQKAIDRWGV................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE ENOLASE]
uniref90: .......................IVASYYLRLE....PYEKAKSFAIGQSLG...........RKKYMGKIVNIVE............IFSIAYPFDNFGP.......KFPMIMTTLLGNASTS...TQAKLIDIYMPKKFTDMFNGPNFGIEGLREVSGVK....RPILLNMIKPCLGFKAEAGAEIFYQTALGVDLIKDDELLANPSYCTLEDRLDKYIEASNRAYEETGKKTLYVPNITDH.VDKILDNAKMAVDK..........LVMLNFASVGIDVLQYLTKN..DVPVIAHYASAGPYYE...FSGIASNLFGKFARMAGADVVM..............YLRTAHELML.............SYKK................................................................................................. [uniref90|F0H203 2,3-diketo-5-methylthiopentyl-1-phosphate enolase family protein n=2 Tax=Anaerococcus hydrogenalis RepID=F0H203_9FIRM]
3FK4-A  : ......................GIIATYLIHDD....LEKKAEQIALGLTIG...........LKQHKGNVIHVEE............IIKIEYPLLNFSP.......DLPAILTTTFGKLSLD...GEVKLIDLTFSDELKKHFPGPKFGIDGIRNLLQVH....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENALTPLTKRIVSGKEVLQSVYETYGHKTLYAVNLTGR.TFDLKENAKRAVQA..........ILLFNVFAYGLDVLQSLAED..PVPIMAHPAVSGAYSA...LYGVSSPLLGKLLRYAGADFSL..............ALAISKYLTE...........DASFKKSFSVPSAGIHPGFVPFIVRDF.GKDVVINAGGGIHGHPNGAQGGGKAFRTAIDATLQNKPLHEV..DDINLHSALQIWG.................. [: RUBISCO-LIKE PROTEIN]
uniref90: ......................GITATYLIHDD....LNQKAEQIALGLTVG...........LKQHKGNVIHVEE............LIKIQYPSVNFSP.......DLPAILTTTFGKLSLD...GEVKLVDLTFSDDLKKHFPGPKFGIEGIRNLLHIQ....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENSLTPLTKRIHAGKEVLQSVYETYGHKTLYAVNLTGR.TYDLKENAKRAIEY..........ILLFNVFAYGLDVLQSLAED..SIPIMAHPAVSGAYAS...LYGFSYSLLGKLLRYAGADFSL..............ALLITHKLTE...........DPSLKRSFPVPSAGIHPGFVPFILRDF.GKNVVINAGGGIHGHPAGAQGGGKAFRAAIDATLQGTPLHEV..GNVDLHAALQLWG.................. [uniref90|C2WBF2 2,3-diketo-5-methylthiopentyl-1-phosphate enolase n=4 Tax=Bacillus RepID=C2WBF2_BACCE]

NOTE: To save space, only 20 of 1109 template profile alignments are shown above. The complete set of alignments can be found in the file Homology_5hqm-~_profile.ali. The template profile contains structural alignments of 16 PDB files, which provide safe anchors for the remaining sequence-based alignments (only reliable regions shown).

In the alignment above, 455 of 470 target residues (96.8%) are aligned to template residues. Among these aligned residues, the sequence identity is 65.1% and the sequence similarity is 76.7% ('similar' means that the BLOSUM62 score is > 0). The following 3 loops had to be modeled (only the first of 2 similar loops in the homodimer is listed):

LoopN-terminal anchorLoop sequenceC-terminal anchor
1LETFAKYNSASHV
3KLIPAKGHGFLEV
5EIDETAFGDDPVKGGGLFKV

After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).

The resulting half-refined model has been saved as Homology_5hqm-~01_refined050.yob and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals0.185Optimal
Packing 1D-0.908Good
Packing 3D-1.328Satisfactory
Overall-0.944Good

Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as Homology_5hqm-~01_refined100.yob, the corresponding Z-scores are listed below:

Check typeQuality Z-scoreComment
Dihedrals0.575Optimal
Packing 1D-0.599Good
Packing 3D-1.361Satisfactory
Overall-0.783Good

Since the overall quality Z-score improved to -0.783 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.

The final model for this template and alignment has been saved as Homology_5hqm-~01.yob, and is shown below, together with a plot of its overall quality Z-score, shown per residue:

6.6. Homology model 6/15, based on template 5HQM-~, alignment variant 02

This model is a homodimer, and based on the following profile-profile alignment:

(To improve readability, only up to ten lines of the complete target multiple sequence alignment (MSA) shown above are also displayed here (upside down). The template MSA has been shrunk and focused on structurally aligned PDB entries. The actual target-template alignment can be found in the middle at the line named 'Match'.)

Q08EW6  : .......................................................................................................................NNQGGGDIEHAKIHGIYMPERAIQLFDGPSKDISDMWRILGRPVKDGGYNAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEIQGNQVFSPMNQTIPLVVDAMKRAQDETGQAKLFSANITADDQYEMCARADFILEAFGP..DADKVAFLVDGYVGDPGMITTARSQYPNQYLHYHRAGHGAVNSPKIKRGYTAFVLAKMSRLQGASGAHVGTMGYGKME................................................................................................................................ [uniref90|Q08EW6 Ribulose 1,5-bisphosphate carboxylase/oxygenase large subunit (Fragment) n=1 Tax=uncultured marine bacterium RepID=Q08EW6_9BACT]
Q5DVV5  : ............................................................................................................................................................................IIKPKLGLRPKPFAEACYNFWLGGDFIKNDEPQGNQIWGPIKEVVPLVKDSLVRAQDDTGMAKLFSFNITADDHYEMLHRGEYILETFAEFSE..NIAFLVDGCVGGPGMVTTARRNFPDQFLHYHRAGHGAVTSDQSDRGYNMLVHMKMARLQGASGIHTGTMGYGKMEGAADDKVIAYMLERDSADGLSYHQEWEGMKATTPIICGGMNA...................................................................................... [uniref90|Q5DVV5 Ribulose-1,5-bisphosphate carboxylase oxygenase large subunit (Fragment) n=11 Tax=uncultured prokaryote RepID=Q5DVV5_9ZZZZ]
Q933G7  : ........................................................................................................................................VPPAYLRLFDGPSTTIKDLWRVLGRPVVDGGFIVGTIIKPKLGLRPQPFADACYDFWLGGDFIKNDEPQGNQVFAPFKDTVRAVNDAMRRAQDATGQPKLFSFNITADDHYEMLARGEYILETFGE..NADHVAFLVDGYVAGPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHVGTMGYGKMEGEASDRDSAFMITQDSAEGPYFKQEW...................................................................................................... [uniref90|Q933G7 Form II ribulose 1,5-bisphosphate carboxylase/oxygenase (Fragment) n=5 Tax=Rhodopseudomonas palustris RepID=Q933G7_RHOPA]
F2ZCE9  : .....................................................................................................................................DFYVPPDFLRLFDGPATTISNLWRVLGRPHQNGGFIVGTIVKPKLGLRPRPFADACYDFWLGGDFIKNDEPQGNQTFSPLKETIPLVADAMRRAQDETGEAKLFSANITADDHYEMVARGEFILDTFGEF..ADHVAFLVDGYVAGAAAVTTARRSFPQQYLHYHRAGHGAITSPQSKRGYTAFVHCKMARLQGASGIHTGTMSFGKMEGEAADRAIAFMLEQDSADGPYFHQEWHGMNPTTSIISG.......................................................................................... [uniref90|F2ZCE9 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=1 Tax=uncultured bacterium RepID=F2ZCE9_9BACT]
F2ZCD0  : ......................................................................................................................GNNQGMGDIANAQMQDFYVPPAMLALFDGPAKSINDLWTLLGRDNENGGYIAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEPQGNQVFCPLKKVLPLVHDAMKRAQDETGEAKLFSLNITADDHYEMCARADFGLETFGE..DAPRLAFLVDGFVGGPGMVTTARRQYSSQYLHYHRAGHGMITSPSSKRGYTAYILAKMSRLMGASGIHVGTMGYGKMEGGADDKIIAYMIERDECQGPFYYQKWHGMKPTTPIVSGGM........................................................................................ [uniref90|F2ZCD0 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=4 Tax=uncultured bacterium RepID=F2ZCD0_9BACT]
F5BZE6  : ......................................................................................................................GNNQGMGDVEYAKMIDFYMARSLLTLFDGPAMNITDMWRVLGRPQVNGGMVVGTIIKPKLGLRPKPFADACYMFWMGGDFIKNDEPQGNQVFAPTREIIPLVAEAMERAQQETGEAKIFSANITADDPFEMIRRGEFILEAFGK..NASHVAFLVDGYVGGPSAVTLCRRYFPNQFLHYHRAGHGAVTSNQSKRGYTVLTHMKMSRLQGASGIHTGTMGYGKMEGDKNEKMVAYMIERDEAMGVYYNQPWHGMTATTPIISGGMNALR.................................................................................... [uniref90|F5BZE6 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II (Fragment) n=1 Tax=alpha proteobacterium LM-5 RepID=F5BZE6_9PROT]
Q9FPW1  : LDQSSRYADLSLDEATLVKNGKHVLVAYIMKPKAGYDYLATAAHFAAESSTGTNVNVCTTDDFTKSVDALVYYIDPDSEE.........MKIAYPTLLFDRNIIDGRGMMCSFLTLAIGNNQGMGDVEYGKIYDFYLPPSFLRLYDGPAVNVEDMWRILGKGTSNGGLVDGTIIKPKLGLQPNPFGEACYSFWQGGDFIKNDEPQGNQVFCQMNECIPEVVKAMRACVKETGSSKLFSANITADDPEEMIARGKYIMSQFGPLSE..NCAFLVDGYVAGGTAVTCCRRNFPKQFLHYHRAGHGSVTSPQTQRGYTAFVHTKISRVIGASGIHVGTMSFGKMEGDASDKNIAYMLQDDEADGPYYRQEWQGMKETTPIISGGMNALRLPAFFENLGHSNVILTAGGGSFGHKDGPKIGAISCRQGEEAWKSLSDVIEYAKTHEEIKGAFLTFQKDADQIYPGWKEKLG... [uniref90|Q9FPW1 Ribulose 1,5-bisphosphate carboxylase oxygenase large subunit n=1 Tax=Symbiodinium sp. RepID=Q9FPW1_SYMSP]
E6VVI6  : .DQTSRYVNFDLKEDQLIADGNHVLCAYIYKPANGYGNVEVAAHFAAESSTGTNVEVCTTDDFTKGVDALVYEVSDASNGDS......LMKIAYPVELFDRNIIDGRAMLASFLTLCIGNNQGMGDVAYAKMHDFYVPRQYLELFDGPSKNIADFWRMLGRPTENGGMIAGTIVKPKLGLRPKPFADACYHFWLGGDFVKNDEPQGNQVFAPLKETITAVADAMRRAQDETGEAKIFSANITADDPREMIARGEFILNAFGE..NASRVAFLVDGYVAGPTAITTARRNFPNQFLHYHRAGHGAVTSPQAKRGYTAFVLSKMSRLQGASGIHTGTMGFGKMEGEMADKSMAYMIEREEAQGPYFKQKWYGMKATTPMISGGMNALRLPGFFDNLGHSNICQTSGGGAFGHLDGPTAGALSLRQSHDAWIQGVNLLDYAKEHNELARAFESFPGDADRFYPTWRHQL.... [uniref90|E6VVI6 Ribulose-bisphosphate carboxylase n=1 Tax=Desulfovibrio aespoeensis Aspo-2 RepID=E6VVI6_DESAO]
Q8RTI1  : MDQSNRYADLSLKEDDLIKGGNHVLVAYLMKPKTGYGYLEAAAHFSAESSTGTNVEVSTTDDFTKGVDALVYEIDEAK.........EIMKIAYPVDLFDRNITDGRAMIVSFLTLAIGNNQGMGDIAYAKMLDFYVPQKYLRLFDGPSKDISDLWRILGRPVVNGGYIAGTIIKPKLGLRPKPFAEAAYQFWLGGDFIKNDEPQGNQVFSPMRETIPLVYDSMKRAMDETGEAKLFSANITADDHYEMMARGEFILNTFGP..DADKVAFLVDGYVGGPGMVTTARRHFANQYLHYHRAGHGAVTSPSAKRGYTAFVLAKMSRLQGASGIHVGTMGYGKMEGDATDKNIAYMIERDSADGPFYHQEWYGMKPTTPIISGGMNALRLPGFFENLGHANLINTSGGGSYGHIDSPAAGAISLRQAYECWQQGADPIEFAKEHKEFARAFESFPGDADTIFPGWREKLGVHK [uniref90|Q8RTI1 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II n=1 Tax=magnetite-containing magnetic vibrio RepID=Q8RTI1_9PROT]
Q0F2Z8  : MDQSNRYADLSLNEADLIAGGKHLLVAYKLIPAKGYGFLEVAAHIAAESSTGTNVEVSTTDDFTRGVDALVYDIDETAFGDEGVTGGGLMKVAYPVELFDPNLIDGHYNVSHMWSLILGNNQGMGDHEGLRMLDFMVPECMIRKFDGPSAGIADLWKVLGRPEVDGGYISGTIIKPKLGLRPEPFAKACLDFWLGGDFIKNDEPQANQPFCPMKVVIPKVAEAMDRAQQETGQAKLFSANATADYHGECVARGEYILSEFAKYGNEKHVAFLIDGFVTGPAGVTTARRAFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLARLQGASGIHTGTMGYGKMEGHGKETVLAYMLERDECMGHYFNQKWYGMKPTAPIISGGMNALRLPGFFENLGHGNVINTCGGGSFGHIDSPAAGGKSLDQAYDCWKSGTDPIEYAKTHGEFARAFESFPGDADKLYPGWRDKLGVHK [uniref90|Q0F2Z8 Ribulose-bisphosphate carboxylase n=1 Tax=Mariprofundus ferrooxydans PV-1 RepID=Q0F2Z8_9PROT]
SecStr  : CCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCEEECCCCCCHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCEEEECCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEECCCCCCHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCHHCCCCCCCEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHHHHCCCC [Secondary structure predicted by PsiPred]
Target  : MDQSNRYANLNLKEEDLIKNGKHLLVAYKLIPAKGHGFLEVAAHVAAESSTGTNVEVSTTDDFTRGVDALVYEIDETAFGDDPVKGGGLFKVAYPVELFDPNLTDGTYNISHMWSLILGNNQGMGDHQGLRMLDFLVPEMMVRKFDGPSANISNLWKVLGRSETDGGYIAGTIIKPKLGLRPEPFAKACYDFWLGGDFIKNDEPQANQPFCPMEVVMPKVAEAMDRAQQATGQAKLFSANITADYYKEMIHRGDFVLETFAKYNSASHVAFLVDGFVTGPAGVTTARREFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLVRLMGASGMHTGTMGYGKMEGHGKETVLAYMLERDECQGPYFYQKWYGMKATTPIISGGMNALRLPGFFQNLGHGNVINTCGGGAFGHIDSPAAGGISLGQAYDCWKSGSDPIEYAKTHKEFARAFESFPKDGDKLFAGWREKLGVHK
Match   : MDQSNRYANLNLKE:|LI :G|H:L AY | P    :F||:AAH AAESSTGTNVEVSTTDDFTRGVDALVYE| | A         :L:K|AYP|ELFD N: DG   I: : :L |GNNQGMGD |  |M DF VP   :| FDGPS::I::LW|VLGR   :GG|I:GTIIKPKLGLRP|PFA:ACYDFWLGGDFI:NDEPQ:NQ F:P:: ::  VA|AM RAQ: TG|AKLFS NITAD | EM| RG|F|LETFA   :A:H|AFLVDG|V:GPA:VTTARR FP  |LH|HRAGHGAVTS :S  G   :   K|:RL:GASG:HTGTMG|GKMEG:: | :|AYM| :D ::GPYF|Q:W GM: TTPIISGGMNALR|PGFF:NLGH:N:I T:GGGAFGH|D: AAG: SL QA :CWK:G:DP|E|AK H|EFARAFESFP:D:DKL| :WR KLGV: 
Template: MDQSNRYANLNLKESELIAGGRHVLCAYIMKPK...NFIQTAAHFAAESSTGTNVEVSTTDDFTRGVDALVYEV.DEAN........SLMKIAYPIELFDRNVIDGRAMIASFLTLTIGNNQGMGDVEYAKMYDFYVPPAYLKLFDGPSTTIKDLWRVLGRPVINGGFIVGTIIKPKLGLRPQPFANACYDFWLGGDFIXNDEPQGNQVFAPFKDTVRAVADAMRRAQDKTGEAKLFSFNITADDHYEMLARGEFILETFAD..NADHIAFLVDGYVAGPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHTGTMGFGKMEGEAADRAIAYMITEDAADGPYFHQEWLGMNPTTPIISGGMNALRMPGFFDNLGHSNLIMTAGGGAFGHVDGGAAGAKSLRQAEQCWKQGADPVEFAKDHREFARAFESFPQDADKLYPNWRAKLGVED
SecStr  : CCCCCCEEETTTHHHHHHHHCCCEEEEEEEECT...HHHHHHHHHHHHHCCCCCCCTTTTHHHHHHCCCEEEEE.ETTT........EEEEEEETTTTCCCCCCCCCCCHHHHHHHHHGGGGCTTTTEEEEEEEEECTTTTTTTTCCCCCCHHHHHHHHHCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCEEEEETTTTCCTTTTHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCHHHHHHHHHHHHHHHHHC..TTTEEEEEEHHHHHCHHHHHHHHHHHCCCEEEEETTTTCCCCTTTTCCCCHHHHHHHHHHHHHCEEEEECTTTTCCCCCTTTTHHHHHHHHHEEEECCCEEEEETTTCCCEEEECCCCCCCHHHHHHHHHHCCCEEEEETTTTCCCCCHHHHHHHHHHHHHHHHHHCCHHHHHHCCHHHHHHHHHHCHHHHHHHHCHHHHHHCCCC [Secondary structure assigned by YASARA]
1RSC-G  : ....LTYYTPDYTP.....KDTDLLAAFRFSPQ....ADEAGAAIAAESST..........TDMDRYKGKCYHI.EP...........FAFIAYPLDLFEE.......SVTNILTSIVGNVFGFKAIRSLRLEDIRFPVALVKTFQGPPHGIQVERDLLNKY....RPMLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKSQAETGEIKGHYLNVTAPTCEEMMKRAEFAKEL..........IIMHDFLTAGFTANTTLAKWCRGVLLHIHRAMHAVIDR...NHGIHFRVLAKCLRLSGGDHLH..............TLGFVDLMREDHIEA.FFTQDWASMPGVLPVASGGIHVWHMPALVEIF.GDDSVLQFGGGTLGHPWGNAPGATANRVALEACVQ...LREAGKWSPELAAALDLW................... [: RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (LARGE]
1GEH-B  : ..........GYEP.......RDIIAVFRVTPA....IEQAAGAVAAESST.GTWT..YEQERWADLSAKAYDF.HD...........IVRIAYPFHAFEE.......NLPGLLASIAGNIFGMKRVKGLRLEDLYFPEKLIREFDGPAFGIEGVRKMLEIK....RPIYGVVPKPKVGYSPEEFEKLAYDLLSNADYMKDDENLTSPWYNRFEERAEIMAKIIDKVENETGEKKTWFANITAD.LLEMEQRLEVLADL..........HAMVDVVITGWGALRYIRDLAAGLAIHGHRAMHAAFTR...YHGISMFVLAKLYRLIGIDQLH..............VIQNARILRESHYK...LEQKFYSIKAAFPTSSGGLHPGNIQPVIEAL.GTDIVLQLGGGTLGHPDGPAAGARAVRQAIDAIMQGIPLDEYAKTHKELARALEKW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE]
1SVD-A  : .....TYWMPEYTP.....LDSDILACFKITPQ....REEAAAAVAAESSTG..........DMDYYKGRAYRI.ED...........YAFIAYPIDLFEE.......SVVNVFTSLVGNVFGFKAVRGLRLEDVRFPLAYVKTCGGPPHGIQVERDKMNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFMRWRDRFLFVQDATETAEAQTGERKGHYLNVTAPTPEEMYKRAEFAKEI..........IIMHDYITGGFTANTGLAKWCQGVLLHIHRAMHAVIDR...NHGIHFRVLTKILRLSGGDHLH..............TLGWIDLLRESFIP..FFDQDWGSMPGVFAVASGGIHVWHMPALVNIF.GDDSVLQFGGGTLGHPWGNAAGAAANRVALEACVE...LTAAAQHSPELKIAMETW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE]
2YBV-A  : ......YYTPDYTP.....KDTDILAAFRVTPQ....FEEAAAAVAAESSTG........LTDLDRYKGCCYDI.EP...........IAYIAYPLDLFEE.......SVTNMLTSIVGNVFGFKALKALRLEDLRIPVAYLKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKAQAETGEIKGHYLNVTAPTCEEMLKRAEFAKEL..........IIMHDFLTAGFTANTTLSKWCRGMLLHIHRAMHAVMDR...NHGIHFRVLAKCLRMSGGDHIH..............TLGFVDLLRENYIE..YFTQDWASMPGVMAVASGGIHVWHMPALVDIF.GDDAVLQFG.....HPWGNAPGATANRVALEACIQ...IREAARWSPELAAAC...................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN]
1BXN-C  : ....MGYWDGDYVP.....KDTDLLALFRITPQ....PVEAAAAVAGESST..WTV......ACDMYRAKAYRV.DP...........FCYVAYDLSLFEE.......SIANLTASIIGNVFSFKPIKAARLEDMRFPVAYVKTFAGPSTGIIVERERLDKF....RPLLGATTKPKLGLSGRNYGRVVYEGLKGLDFMKDDENINSQPFMHWRDRFLFVMDAVNKASAATGEVKGSYLNVTAGTMEEMYRRAEFAKSL..........IIMVD.LIVGWTCIQSMSNWCRDMILHLHRAGHGTYTR...NHGVSFRVIAKWLRLAGVDHMH..............VQGYYNVCRDAYTQ..FFDQDWASLRKVMPVASGGIHAGQMHQLIHLF.GDDVVLQFGGGTIGHPQGIQAGATANRVALEAMVL...LRDAARWCGPLRAALDTW................... [: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)]
1EJ7-L  : .....TYYTPEYQT.....KDTDILAAFRVTPQ....PEEAGAAVAAESSTGTWTTV.....SLDRYKGRCYRI.ER...........IAYVAYPLDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENVNSQPFMRWRDRFLFCAEALYKAQAETGEIKGHYLNATAGTCEEMIKRAVFAREL..........IVMHDYLTGGFTANTSLAHYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHIH..............TLGFVDLLRDDFVE..YFTQDWVSLPGVLPVASGGIHVWHMPALTEIF.GDDSVLQFGGGTLGHPWGNAPGAVANRVALEACVK...IREACKWSPELAAACEVW................... [: RUBISCO (LARGE SUBUNIT)]
1IWA-C  : ....MGYWNPDYQV.....KDTDVLALFRVTPQ....PIEAAAAVAGESST...........AADLYRAKAYKV.DQ...........FAYIAYELDLFEE.......SIANLTASIIGNVFGFKAVKALRLEDMRLPLAYLKTFQGPATGVILERERLDKF....RPLLGCTTKPKLGLSGKNYGRVVYEALKGLDFVKDDENINSQPFMRWRERYLFTMEAVNKASAATGEVKGHYLNVTAATMEEMYARANFAKEL..........IIMID.LVIGYTAIQTMAKWARDMILHLHRAGNSTYSR...NHGMNFRVICKWMRMAGVDHIH..............TRGFYKTLLLPKLE..FFDMEWASLRKVMPVASGGIHAGQMHQLIHYLG.EDVVLQFGGGTIGHPDGIQAGATANRVALEAMIL...LREAAKTCGALRTALDLW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE]
1TEL-B  : .....GFFAS...........QYLVLDYYLESV....IETALAHFCSEQSTA........DEDFRVHAAKVIDY.EV...........RVTIAHPHCNFGP.......KIPNLLTAVCGETYFTPGVPVVKLMDIHFPDTYLADFEGPKFGIEGLRDILNAH....RPIFFGVVKPNIGLSPGEFAEIAYQSWLGLDIAKDDEMLADVTWSSIEERAAHLGKARRKAEAETGEPKIYLANITDE.VDSLMEKHDVAVRN..........ALLINALPVGLSAVRMLSNYT.QVPLIGHFPFIASFSR...KYGIHSKVMTKLQRLAGLDAVI..............VLENVIECTKP..........MGRIKPCLPVPGGSDSALTLQTVYEKVGNVDFGFVPGRGVFGHPMGPKAGAKSIRQAWEAIEQGISIETWAETHPELQAMVDQ.................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE, LARGE SUBUNIT]
2D69-A  : .....DFVDLNYEP.....GRDELIVEYYFEPN....PEEAAGRIASESSIGTW.........AKRSMAKVFYL.EK...........IAKIAYPLTLFEE.......SLVQLFSAVAGNVFGMKALKNLRLLDFHPPYEYLRHFKGPQFGVQGIREFMGVK....RPLTATVPKPKMGWSVEEYAEIAYELWSGIDLLKDDENFTSFPFNRFEERVRKLYRVRDRVEAETGETKEYLINITGP.VNIMEKRAEMVANE..........YVMIDIVVAGWSALQYMREVTEGLAIHAHRAMHAAFTR...RHGITMLALAKAARMIGVDQIH..............IKRINDFLLS...........WEHIRPVFPVASGGLHPGLMPELIRLF.GKDLVIQAGGGVMGHPDGPRAGAKALRDAIDAAIEGVDLDEKAKSSPELKKSLREV................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE]
2QYG-D  : .....GFYAK...........NYIELDFDFECA....PHEAAAHLCSEQSTA...........RPRFAAKVLEL.SA...........RVTIAHPHGNF........AKIPNLLSAVCGEVFFSPGIPLIRLQDIRFPEPYLAAFDGPRFGIAGVRERLQAF....RPIFFGVIKPNIGLPPQPFAELGYQSWTGLDIAKDDEMLADVDWCPLAERAALLGDACRRASAETGVPKIYLANITDE.VDRLTELHDVAVAN..........ALLINAMPVGLSAVRMLRKHA.TVPLIAHFPFIAAFSR...NYGIHSRVMTRLQRLAGFDVVI..............VLDCIRACLE...........MGPIKPCLPVPGGSDSAATLENVYRKVGSADFGFVPGRGVFGHPMGPAAGATSIRQAWDAIAAGIPVPDHAASHPELAAALRAF................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE-LIKE PROTEIN 2]
2V67-A  : ....LTYYTPDYVV......DTDILAAFRMTPQ....PEECGAAVAAESST...........SLDRYKGRCYDI.EP...........IAYVAYXIDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFVGXPHGIQVERDKLNKY....RGLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTXDDENVNSQPFMRWRDRFLFVAEAIYKAQAETGEVKGHYLNATAGTCEEMMKRAVXAKEL..........IIMHDYLTGGFTANTSLAIYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHLH..............ILGFVDLMRDDYVE..YFTQDWXSMPGVMPVASGGIHVWHMPALVEIF.GDDACLQFGGGTLGHPWGNAPGAAANRVALEACTQ...IRSACKWSPELAAACEVW................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN]
3NWR-A  : ....................EDTLEADYLIET.....PARVADVMAGEQSSG............ARSRASVLRI.EE...........RITLSFPLANI.........NLPTLAATVAGNLYDLGEVTGVRLLSLRLPASYRARFELPRHGVAGTRALTDVK....RPMIGTIIKPNVGLSAAETAALVRELCEAVDFIXDDEVCANPAHAPLAERVRAVMSEVRRYRERSGRPVMVAFNITDD.LDAMRRHAELVERE..........CVMASINWCGFSAIQSLRRTT.PLVLHAHRNGYGMMSR...ALGMSFQAYQTLWRLSGVDHMH..............VIESARDCATP...............AVLPAFSSGQWAGTVQATFDAVRSTDLLFMSGGGILAHPDGPAAGVTSVRQAWAAVQAGTPLPVYAEHMPELRRALAFF................... [: A RUBISCO-LIKE PROTEIN]
3QFW-B  : ......................RIVATYHIAS.....IEQRALALAIEQSVEC............NIVGRVEDV.AE...........AVRIGLAAATAP.......AEPGQLLNMLFGNSSIQPD...IALADVELPAHYLTAFGGPRVGLAGIRTLTGAQ....RALTASALKP.QGLSPAALASIAHQLALGVDLIKDDHGLADQAFSPFAERAAAVGKAVREANAARGGRTLYAPNISG.TLDDMRRQLGVIRDE..........AVLVAPMIVGVSNFHAIVKEAAGLVVVAHPAMAGAA........IAAPLLGRLFRLFGADATV..............CLALAQAARD...........FGKLNACIPTPAGGIMLQRVNELLRFYG.QDVMLLI..........LTEQASRFVNKVADYGQR....................................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE]
uniref90: ......................RIIATYHLAS.....VAERAKGLAIEQSVEC............TIVGRVEDI.AE...........AVRIGLAAATAP.......AEPGQLINMLFGNSSMQQD...VTLVDVELPPSYLAAFGGPRLGLAGLRALTGTQ....RALTASALKP.QGLSPAALARIAGQLARGVDVIKDDHGIADQAYSPFAARVEAVGRAVQEANVARDGHSLYAPNLSG.TLDDMRRQLDLAREQ..........AVMVAPMIVGLANFHAVVKAAAGMVVIAHPALSGVT........IAPPLLGKLFRLFGADATI..............CLQLARAGRD...........WGALEPCMPVPAGGLTADRVAELLQFYG.HDVMLLI..........LTEEAARFVNEVAAHGK........................................ [uniref90|Q07KC6 Ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit n=1 Tax=Rhodopseudomonas palustris BisA53 RepID=Q07KC6_RHOP5]
2ZVI-A  : ......................ELLATYLLT......TEKKAEQIATGLTVG...........MQKHKGRVIKV.EE...........VITIAYPEINFSQ.......DIPALLTTVFGKLSL...DGKIKLIDLHFSEAFKRALPGPKFGVYGIRKLLGE.....RPLLMSIFKGVIGRDLSDIKEQLRQQALGVDLIKDDEIFFETGLAPFETRIAEGKQILKETYEQTGHKTLYAVNLTGR.TADLKDKARRAAEL..........ALLFNVFAYGLDVMQGLAED..PVPIMAHPAVSGAFTS...FYGFSHALLGKLNRYCGADFSL..............ALAIHEECVR.............AFNQTFAVPSAGIHPGMVPLLMRDF.GIDHIINAGGGVHGHPNGAQGGGRAFRAIIDAVLEAQPIDEKAEQCKDLKLALDKWGK................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE]
uniref90: ......................ELLATYVLT......DERKAEQIALGLTVG...........LQKHKGRVEKV.TE...........EVTIAYPEANFSA.......DIPAVLSTIFGKLSL...DGKVKLVDIQFSDRFKKSLPGPVFGIDGIRKKTGV.....RPLLMSIFKGVIGRDMTDLKEQLRLQALGVDFIKDDEILFESPLAPFEDRIKEGKKILKETYEETGHRTLYAVHLTGR.TFELRDRARKAAEL..........ALLFNVFAYGLDVMQSLAED..RLPIMAHPAVSGALTS...EYGFSHSLLGKLNRYAGADLSL..............AFGIYEACVK.............SVQKTFPVPSAGIHPGMVPVLMKDF.GLDHVINAGGGIHGHPRGAIGGGKAFRSIIDAVIHGESIQEKTASCQDLKAALELWGR................. [uniref90|A8FCG8 2,3-diketo-5-methylthiopentyl-1-phosphate enolase n=2 Tax=Bacillus pumilus RepID=MTNW_BACP2]
2OEK-B  : ......................AVMATYLLHDE....IRKKAEGIALGLTIG...........LRKHKGEVVAI.EE...........IVKIAYPTVNFSA.......DLPALLVTTFGKLSLD...GEVRLLDLEFPDEWKRQFPGPRFGIDGIRDRVGVH....RPLLMSIFKGMIGRDLAYLTSELKKQALGVDLVXDDEILFDSELLPFEKRITEGKAALQEVYEQTGKRTLYAVNLTGK.TFALKDKAKRAAEL..........VLLFNVFAYGLDVLQALRED..AVPIMAHPAFSGAVTP...FYGVAPSLWGKLLRLAGADFVL..............ALGIARALTD.............PFARAFPVPSAGIHPGLVPLIIRDF.GLDTIVNAGGGIHGHPDGAIGGGRAFRAAIDAVLAGRPLRAAAAENEALQKAIDRWGV................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE ENOLASE]
uniref90: .......................IVASYYLRLE....PYEKAKSFAIGQSLG...........RKKYMGKIVNI.VE...........IFSIAYPFDNFGP.......KFPMIMTTLLGNASTS...TQAKLIDIYMPKKFTDMFNGPNFGIEGLREVSGVK....RPILLNMIKPCLGFKAEAGAEIFYQTALGVDLIKDDELLANPSYCTLEDRLDKYIEASNRAYEETGKKTLYVPNITDH.VDKILDNAKMAVDK..........LVMLNFASVGIDVLQYLTKN..DVPVIAHYASAGPYYE...FSGIASNLFGKFARMAGADVVM..............YLRTAHELML.............SYKK................................................................................................. [uniref90|F0H203 2,3-diketo-5-methylthiopentyl-1-phosphate enolase family protein n=2 Tax=Anaerococcus hydrogenalis RepID=F0H203_9FIRM]
3FK4-A  : ......................GIIATYLIHDD....LEKKAEQIALGLTIG...........LKQHKGNVIHV.EE...........IIKIEYPLLNFSP.......DLPAILTTTFGKLSLD...GEVKLIDLTFSDELKKHFPGPKFGIDGIRNLLQVH....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENALTPLTKRIVSGKEVLQSVYETYGHKTLYAVNLTGR.TFDLKENAKRAVQA..........ILLFNVFAYGLDVLQSLAED..PVPIMAHPAVSGAYSA...LYGVSSPLLGKLLRYAGADFSL..............ALAISKYLTE...........DASFKKSFSVPSAGIHPGFVPFIVRDF.GKDVVINAGGGIHGHPNGAQGGGKAFRTAIDATLQNKPLHEV..DDINLHSALQIWG.................. [: RUBISCO-LIKE PROTEIN]
uniref90: ......................GITATYLIHDD....LNQKAEQIALGLTVG...........LKQHKGNVIHV.EE...........LIKIQYPSVNFSP.......DLPAILTTTFGKLSLD...GEVKLVDLTFSDDLKKHFPGPKFGIEGIRNLLHIQ....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENSLTPLTKRIHAGKEVLQSVYETYGHKTLYAVNLTGR.TYDLKENAKRAIEY..........ILLFNVFAYGLDVLQSLAED..SIPIMAHPAVSGAYAS...LYGFSYSLLGKLLRYAGADFSL..............ALLITHKLTE...........DPSLKRSFPVPSAGIHPGFVPFILRDF.GKNVVINAGGGIHGHPAGAQGGGKAFRAAIDATLQGTPLHEV..GNVDLHAALQLWG.................. [uniref90|C2WBF2 2,3-diketo-5-methylthiopentyl-1-phosphate enolase n=4 Tax=Bacillus RepID=C2WBF2_BACCE]

NOTE: To save space, only 20 of 1109 template profile alignments are shown above. The complete set of alignments can be found in the file Homology_5hqm-~_profile.ali. The template profile contains structural alignments of 16 PDB files, which provide safe anchors for the remaining sequence-based alignments (only reliable regions shown).

In the alignment above, 456 of 470 target residues (97.0%) are aligned to template residues. Among these aligned residues, the sequence identity is 64.7% and the sequence similarity is 76.5% ('similar' means that the BLOSUM62 score is > 0). The following 4 loops had to be modeled (only the first of 2 similar loops in the homodimer is listed):

LoopN-terminal anchorLoop sequenceC-terminal anchor
1LVYEIDETAFGDD
3LETFAKYNSASHV
5KLIPAKGHGFLEV
7DETAFGDDPVKGGGLFKV

After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).

The resulting half-refined model has been saved as Homology_5hqm-~02_refined050.yob and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals0.013Optimal
Packing 1D-0.826Good
Packing 3D-1.388Satisfactory
Overall-0.965Good

Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as Homology_5hqm-~02_refined100.yob, the corresponding Z-scores are listed below:

Check typeQuality Z-scoreComment
Dihedrals0.313Optimal
Packing 1D-0.438Good
Packing 3D-1.546Satisfactory
Overall-0.844Good

Since the overall quality Z-score improved to -0.844 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.

The final model for this template and alignment has been saved as Homology_5hqm-~02.yob, and is shown below, together with a plot of its overall quality Z-score, shown per residue:

6.7. Homology model 7/15, based on template 5HQM-~, alignment variant 03

This model is a homodimer, and based on the following profile-profile alignment:

(To improve readability, only up to ten lines of the complete target multiple sequence alignment (MSA) shown above are also displayed here (upside down). The template MSA has been shrunk and focused on structurally aligned PDB entries. The actual target-template alignment can be found in the middle at the line named 'Match'.)

Q08EW6  : .......................................................................................................................NNQGGGDIEHAKIHGIYMPERAIQLFDGPSKDISDMWRILGRPVKDGGYNAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEIQGNQVFSPMNQTIPLVVDAMKRAQDETGQAKLFSANITADDQYEMCARADFILEAFGP..DADKVAFLVDGYVGDPGMITTARSQYPNQYLHYHRAGHGAVNSPKIKRGYTAFVLAKMSRLQGASGAHVGTMGYGKME................................................................................................................................ [uniref90|Q08EW6 Ribulose 1,5-bisphosphate carboxylase/oxygenase large subunit (Fragment) n=1 Tax=uncultured marine bacterium RepID=Q08EW6_9BACT]
Q5DVV5  : ............................................................................................................................................................................IIKPKLGLRPKPFAEACYNFWLGGDFIKNDEPQGNQIWGPIKEVVPLVKDSLVRAQDDTGMAKLFSFNITADDHYEMLHRGEYILETFAEFSE..NIAFLVDGCVGGPGMVTTARRNFPDQFLHYHRAGHGAVTSDQSDRGYNMLVHMKMARLQGASGIHTGTMGYGKMEGAADDKVIAYMLERDSADGLSYHQEWEGMKATTPIICGGMNA...................................................................................... [uniref90|Q5DVV5 Ribulose-1,5-bisphosphate carboxylase oxygenase large subunit (Fragment) n=11 Tax=uncultured prokaryote RepID=Q5DVV5_9ZZZZ]
Q933G7  : ........................................................................................................................................VPPAYLRLFDGPSTTIKDLWRVLGRPVVDGGFIVGTIIKPKLGLRPQPFADACYDFWLGGDFIKNDEPQGNQVFAPFKDTVRAVNDAMRRAQDATGQPKLFSFNITADDHYEMLARGEYILETFGE..NADHVAFLVDGYVAGPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHVGTMGYGKMEGEASDRDSAFMITQDSAEGPYFKQEW...................................................................................................... [uniref90|Q933G7 Form II ribulose 1,5-bisphosphate carboxylase/oxygenase (Fragment) n=5 Tax=Rhodopseudomonas palustris RepID=Q933G7_RHOPA]
F2ZCE9  : .....................................................................................................................................DFYVPPDFLRLFDGPATTISNLWRVLGRPHQNGGFIVGTIVKPKLGLRPRPFADACYDFWLGGDFIKNDEPQGNQTFSPLKETIPLVADAMRRAQDETGEAKLFSANITADDHYEMVARGEFILDTFGEF..ADHVAFLVDGYVAGAAAVTTARRSFPQQYLHYHRAGHGAITSPQSKRGYTAFVHCKMARLQGASGIHTGTMSFGKMEGEAADRAIAFMLEQDSADGPYFHQEWHGMNPTTSIISG.......................................................................................... [uniref90|F2ZCE9 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=1 Tax=uncultured bacterium RepID=F2ZCE9_9BACT]
F2ZCD0  : ......................................................................................................................GNNQGMGDIANAQMQDFYVPPAMLALFDGPAKSINDLWTLLGRDNENGGYIAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEPQGNQVFCPLKKVLPLVHDAMKRAQDETGEAKLFSLNITADDHYEMCARADFGLETFGE..DAPRLAFLVDGFVGGPGMVTTARRQYSSQYLHYHRAGHGMITSPSSKRGYTAYILAKMSRLMGASGIHVGTMGYGKMEGGADDKIIAYMIERDECQGPFYYQKWHGMKPTTPIVSGGM........................................................................................ [uniref90|F2ZCD0 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=4 Tax=uncultured bacterium RepID=F2ZCD0_9BACT]
F5BZE6  : ......................................................................................................................GNNQGMGDVEYAKMIDFYMARSLLTLFDGPAMNITDMWRVLGRPQVNGGMVVGTIIKPKLGLRPKPFADACYMFWMGGDFIKNDEPQGNQVFAPTREIIPLVAEAMERAQQETGEAKIFSANITADDPFEMIRRGEFILEAFGK..NASHVAFLVDGYVGGPSAVTLCRRYFPNQFLHYHRAGHGAVTSNQSKRGYTVLTHMKMSRLQGASGIHTGTMGYGKMEGDKNEKMVAYMIERDEAMGVYYNQPWHGMTATTPIISGGMNALR.................................................................................... [uniref90|F5BZE6 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II (Fragment) n=1 Tax=alpha proteobacterium LM-5 RepID=F5BZE6_9PROT]
Q9FPW1  : LDQSSRYADLSLDEATLVKNGKHVLVAYIMKPKAGYDYLATAAHFAAESSTGTNVNVCTTDDFTKSVDALVYYIDPDSEE.........MKIAYPTLLFDRNIIDGRGMMCSFLTLAIGNNQGMGDVEYGKIYDFYLPPSFLRLYDGPAVNVEDMWRILGKGTSNGGLVDGTIIKPKLGLQPNPFGEACYSFWQGGDFIKNDEPQGNQVFCQMNECIPEVVKAMRACVKETGSSKLFSANITADDPEEMIARGKYIMSQFGPLSE..NCAFLVDGYVAGGTAVTCCRRNFPKQFLHYHRAGHGSVTSPQTQRGYTAFVHTKISRVIGASGIHVGTMSFGKMEGDASDKNIAYMLQDDEADGPYYRQEWQGMKETTPIISGGMNALRLPAFFENLGHSNVILTAGGGSFGHKDGPKIGAISCRQGEEAWKSLSDVIEYAKTHEEIKGAFLTFQKDADQIYPGWKEKLG... [uniref90|Q9FPW1 Ribulose 1,5-bisphosphate carboxylase oxygenase large subunit n=1 Tax=Symbiodinium sp. RepID=Q9FPW1_SYMSP]
E6VVI6  : .DQTSRYVNFDLKEDQLIADGNHVLCAYIYKPANGYGNVEVAAHFAAESSTGTNVEVCTTDDFTKGVDALVYEVSDASNGDS......LMKIAYPVELFDRNIIDGRAMLASFLTLCIGNNQGMGDVAYAKMHDFYVPRQYLELFDGPSKNIADFWRMLGRPTENGGMIAGTIVKPKLGLRPKPFADACYHFWLGGDFVKNDEPQGNQVFAPLKETITAVADAMRRAQDETGEAKIFSANITADDPREMIARGEFILNAFGE..NASRVAFLVDGYVAGPTAITTARRNFPNQFLHYHRAGHGAVTSPQAKRGYTAFVLSKMSRLQGASGIHTGTMGFGKMEGEMADKSMAYMIEREEAQGPYFKQKWYGMKATTPMISGGMNALRLPGFFDNLGHSNICQTSGGGAFGHLDGPTAGALSLRQSHDAWIQGVNLLDYAKEHNELARAFESFPGDADRFYPTWRHQL.... [uniref90|E6VVI6 Ribulose-bisphosphate carboxylase n=1 Tax=Desulfovibrio aespoeensis Aspo-2 RepID=E6VVI6_DESAO]
Q8RTI1  : MDQSNRYADLSLKEDDLIKGGNHVLVAYLMKPKTGYGYLEAAAHFSAESSTGTNVEVSTTDDFTKGVDALVYEIDEAK.........EIMKIAYPVDLFDRNITDGRAMIVSFLTLAIGNNQGMGDIAYAKMLDFYVPQKYLRLFDGPSKDISDLWRILGRPVVNGGYIAGTIIKPKLGLRPKPFAEAAYQFWLGGDFIKNDEPQGNQVFSPMRETIPLVYDSMKRAMDETGEAKLFSANITADDHYEMMARGEFILNTFGP..DADKVAFLVDGYVGGPGMVTTARRHFANQYLHYHRAGHGAVTSPSAKRGYTAFVLAKMSRLQGASGIHVGTMGYGKMEGDATDKNIAYMIERDSADGPFYHQEWYGMKPTTPIISGGMNALRLPGFFENLGHANLINTSGGGSYGHIDSPAAGAISLRQAYECWQQGADPIEFAKEHKEFARAFESFPGDADTIFPGWREKLGVHK [uniref90|Q8RTI1 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II n=1 Tax=magnetite-containing magnetic vibrio RepID=Q8RTI1_9PROT]
Q0F2Z8  : MDQSNRYADLSLNEADLIAGGKHLLVAYKLIPAKGYGFLEVAAHIAAESSTGTNVEVSTTDDFTRGVDALVYDIDETAFGDEGVTGGGLMKVAYPVELFDPNLIDGHYNVSHMWSLILGNNQGMGDHEGLRMLDFMVPECMIRKFDGPSAGIADLWKVLGRPEVDGGYISGTIIKPKLGLRPEPFAKACLDFWLGGDFIKNDEPQANQPFCPMKVVIPKVAEAMDRAQQETGQAKLFSANATADYHGECVARGEYILSEFAKYGNEKHVAFLIDGFVTGPAGVTTARRAFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLARLQGASGIHTGTMGYGKMEGHGKETVLAYMLERDECMGHYFNQKWYGMKPTAPIISGGMNALRLPGFFENLGHGNVINTCGGGSFGHIDSPAAGGKSLDQAYDCWKSGTDPIEYAKTHGEFARAFESFPGDADKLYPGWRDKLGVHK [uniref90|Q0F2Z8 Ribulose-bisphosphate carboxylase n=1 Tax=Mariprofundus ferrooxydans PV-1 RepID=Q0F2Z8_9PROT]
SecStr  : CCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCEEECCCCCCHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCEEEECCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEECCCCCCHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCHHCCCCCCCEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHHHHCCCC [Secondary structure predicted by PsiPred]
Target  : MDQSNRYANLNLKEEDLIKNGKHLLVAYKLIPAKGHGFLEVAAHVAAESSTGTNVEVSTTDDFTRGVDALVYEIDETAFGDDPVKGGGLFKVAYPVELFDPNLTDGTYNISHMWSLILGNNQGMGDHQGLRMLDFLVPEMMVRKFDGPSANISNLWKVLGRSETDGGYIAGTIIKPKLGLRPEPFAKACYDFWLGGDFIKNDEPQANQPFCPMEVVMPKVAEAMDRAQQATGQAKLFSANITADYYKEMIHRGDFVLETFAKYNSASHVAFLVDGFVTGPAGVTTARREFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLVRLMGASGMHTGTMGYGKMEGHGKETVLAYMLERDECQGPYFYQKWYGMKATTPIISGGMNALRLPGFFQNLGHGNVINTCGGGAFGHIDSPAAGGISLGQAYDCWKSGSDPIEYAKTHKEFARAFESFPKDGDKLFAGWREKLGVHK
Match   : MDQSNRYANLNLKE:|LI :G|H:L AY | P    :F||:AAH AAESSTGTNVEVSTTDDFTRGVDALVYE|DE:          :L:K|AYP|ELFD N: DG   I: : :L |GNNQGMGD |  |M DF VP   :| FDGPS::I::LW|VLGR   :GG|I:GTIIKPKLGLRP|PFA:ACYDFWLGGDFI:NDEPQ:NQ F:P:: ::  VA|AM RAQ: TG|AKLFS NITAD | EM| RG|F|LETFA   :A:H|AFLVDG|V:GPA:VTTARR FP  |LH|HRAGHGAVTS :S  G   :   K|:RL:GASG:HTGTMG|GKMEG:: | :|AYM| :D ::GPYF|Q:W GM: TTPIISGGMNALR|PGFF:NLGH:N:I T:GGGAFGH|D: AAG: SL QA :CWK:G         H|EFARAFESFP:D:DKL| :WR KLGV: 
Template: MDQSNRYANLNLKESELIAGGRHVLCAYIMKPK...NFIQTAAHFAAESSTGTNVEVSTTDDFTRGVDALVYEVDEA..........SLMKIAYPIELFDRNVIDGRAMIASFLTLTIGNNQGMGDVEYAKMYDFYVPPAYLKLFDGPSTTIKDLWRVLGRPVINGGFIVGTIIKPKLGLRPQPFANACYDFWLGGDFIXNDEPQGNQVFAPFKDTVRAVADAMRRAQDKTGEAKLFSFNITADDHYEMLARGEFILETFAD..NADHIAFLVDGYVAGPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHTGTMGFGKMEGEAADRAIAYMITEDAADGPYFHQEWLGMNPTTPIISGGMNALRMPGFFDNLGHSNLIMTAGGGAFGHVDGGAAGAKSLRQAEQCWKQG..DPVEFA.HREFARAFESFPQDADKLYPNWRAKLGVED
SecStr  : CCCCCCEEETTTHHHHHHHHCCCEEEEEEEECT...HHHHHHHHHHHHHCCCCCCCTTTTHHHHHHCCCEEEEEETT..........EEEEEEETTTTCCCCCCCCCCCHHHHHHHHHGGGGCTTTTEEEEEEEEECTTTTTTTTCCCCCCHHHHHHHHHCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCEEEEETTTTCCTTTTHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCHHHHHHHHHHHHHHHHHC..TTTEEEEEEHHHHHCHHHHHHHHHHHCCCEEEEETTTTCCCCTTTTCCCCHHHHHHHHHHHHHCEEEEECTTTTCCCCCTTTTHHHHHHHHHEEEECCCEEEEETTTCCCEEEECCCCCCCHHHHHHHHHHCCCEEEEETTTTCCCCCHHHHHHHHHHHHHHHHHHC..HHHHHH.HHHHHHHHHHCHHHHHHHHCHHHHHHCCCC [Secondary structure assigned by YASARA]
1RSC-G  : ....LTYYTPDYTP.....KDTDLLAAFRFSPQ....ADEAGAAIAAESST..........TDMDRYKGKCYHIEP............FAFIAYPLDLFEE.......SVTNILTSIVGNVFGFKAIRSLRLEDIRFPVALVKTFQGPPHGIQVERDLLNKY....RPMLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKSQAETGEIKGHYLNVTAPTCEEMMKRAEFAKEL..........IIMHDFLTAGFTANTTLAKWCRGVLLHIHRAMHAVIDR...NHGIHFRVLAKCLRLSGGDHLH..............TLGFVDLMREDHIEA.FFTQDWASMPGVLPVASGGIHVWHMPALVEIF.GDDSVLQFGGGTLGHPWGNAPGATANRVALEACVQ....LREAG.SPELAAALDLW................... [: RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (LARGE]
1GEH-B  : ..........GYEP.......RDIIAVFRVTPA....IEQAAGAVAAESST.GTWT..YEQERWADLSAKAYDFHD............IVRIAYPFHAFEE.......NLPGLLASIAGNIFGMKRVKGLRLEDLYFPEKLIREFDGPAFGIEGVRKMLEIK....RPIYGVVPKPKVGYSPEEFEKLAYDLLSNADYMKDDENLTSPWYNRFEERAEIMAKIIDKVENETGEKKTWFANITAD.LLEMEQRLEVLADL..........HAMVDVVITGWGALRYIRDLAAGLAIHGHRAMHAAFTR...YHGISMFVLAKLYRLIGIDQLH..............VIQNARILRESHYK...LEQKFYSIKAAFPTSSGGLHPGNIQPVIEAL.GTDIVLQLGGGTLGHPDGPAAGARAVRQAIDAIMQG..PLDEYA.HKELARALEKW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE]
1SVD-A  : .....TYWMPEYTP.....LDSDILACFKITPQ....REEAAAAVAAESSTG..........DMDYYKGRAYRIED............YAFIAYPIDLFEE.......SVVNVFTSLVGNVFGFKAVRGLRLEDVRFPLAYVKTCGGPPHGIQVERDKMNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFMRWRDRFLFVQDATETAEAQTGERKGHYLNVTAPTPEEMYKRAEFAKEI..........IIMHDYITGGFTANTGLAKWCQGVLLHIHRAMHAVIDR...NHGIHFRVLTKILRLSGGDHLH..............TLGWIDLLRESFIP..FFDQDWGSMPGVFAVASGGIHVWHMPALVNIF.GDDSVLQFGGGTLGHPWGNAAGAAANRVALEACVE....LTAAA.SPELKIAMETW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE]
2YBV-A  : ......YYTPDYTP.....KDTDILAAFRVTPQ....FEEAAAAVAAESSTG........LTDLDRYKGCCYDIEP............IAYIAYPLDLFEE.......SVTNMLTSIVGNVFGFKALKALRLEDLRIPVAYLKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKAQAETGEIKGHYLNVTAPTCEEMLKRAEFAKEL..........IIMHDFLTAGFTANTTLSKWCRGMLLHIHRAMHAVMDR...NHGIHFRVLAKCLRMSGGDHIH..............TLGFVDLLRENYIE..YFTQDWASMPGVMAVASGGIHVWHMPALVDIF.GDDAVLQFG.....HPWGNAPGATANRVALEACIQ....IREAA.SPELAAAC...................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN]
1BXN-C  : ....MGYWDGDYVP.....KDTDLLALFRITPQ....PVEAAAAVAGESST..WTV......ACDMYRAKAYRVDP............FCYVAYDLSLFEE.......SIANLTASIIGNVFSFKPIKAARLEDMRFPVAYVKTFAGPSTGIIVERERLDKF....RPLLGATTKPKLGLSGRNYGRVVYEGLKGLDFMKDDENINSQPFMHWRDRFLFVMDAVNKASAATGEVKGSYLNVTAGTMEEMYRRAEFAKSL..........IIMVD.LIVGWTCIQSMSNWCRDMILHLHRAGHGTYTR...NHGVSFRVIAKWLRLAGVDHMH..............VQGYYNVCRDAYTQ..FFDQDWASLRKVMPVASGGIHAGQMHQLIHLF.GDDVVLQFGGGTIGHPQGIQAGATANRVALEAMVL....LRDAA.CGPLRAALDTW................... [: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)]
1EJ7-L  : .....TYYTPEYQT.....KDTDILAAFRVTPQ....PEEAGAAVAAESSTGTWTTV.....SLDRYKGRCYRIER............IAYVAYPLDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENVNSQPFMRWRDRFLFCAEALYKAQAETGEIKGHYLNATAGTCEEMIKRAVFAREL..........IVMHDYLTGGFTANTSLAHYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHIH..............TLGFVDLLRDDFVE..YFTQDWVSLPGVLPVASGGIHVWHMPALTEIF.GDDSVLQFGGGTLGHPWGNAPGAVANRVALEACVK....IREAC.SPELAAACEVW................... [: RUBISCO (LARGE SUBUNIT)]
1IWA-C  : ....MGYWNPDYQV.....KDTDVLALFRVTPQ....PIEAAAAVAGESST...........AADLYRAKAYKVDQ............FAYIAYELDLFEE.......SIANLTASIIGNVFGFKAVKALRLEDMRLPLAYLKTFQGPATGVILERERLDKF....RPLLGCTTKPKLGLSGKNYGRVVYEALKGLDFVKDDENINSQPFMRWRERYLFTMEAVNKASAATGEVKGHYLNVTAATMEEMYARANFAKEL..........IIMID.LVIGYTAIQTMAKWARDMILHLHRAGNSTYSR...NHGMNFRVICKWMRMAGVDHIH..............TRGFYKTLLLPKLE..FFDMEWASLRKVMPVASGGIHAGQMHQLIHYLG.EDVVLQFGGGTIGHPDGIQAGATANRVALEAMIL....LREAA.CGALRTALDLW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE]
1TEL-B  : .....GFFAS...........QYLVLDYYLESV....IETALAHFCSEQSTA........DEDFRVHAAKVIDYEV............RVTIAHPHCNFGP.......KIPNLLTAVCGETYFTPGVPVVKLMDIHFPDTYLADFEGPKFGIEGLRDILNAH....RPIFFGVVKPNIGLSPGEFAEIAYQSWLGLDIAKDDEMLADVTWSSIEERAAHLGKARRKAEAETGEPKIYLANITDE.VDSLMEKHDVAVRN..........ALLINALPVGLSAVRMLSNYT.QVPLIGHFPFIASFSR...KYGIHSKVMTKLQRLAGLDAVI..............VLENVIECTKP..........MGRIKPCLPVPGGSDSALTLQTVYEKVGNVDFGFVPGRGVFGHPMGPKAGAKSIRQAWEAIEQG..SIETWA.HPELQAMVDQ.................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE, LARGE SUBUNIT]
2D69-A  : .....DFVDLNYEP.....GRDELIVEYYFEPN....PEEAAGRIASESSIGTW.........AKRSMAKVFYLEK............IAKIAYPLTLFEE.......SLVQLFSAVAGNVFGMKALKNLRLLDFHPPYEYLRHFKGPQFGVQGIREFMGVK....RPLTATVPKPKMGWSVEEYAEIAYELWSGIDLLKDDENFTSFPFNRFEERVRKLYRVRDRVEAETGETKEYLINITGP.VNIMEKRAEMVANE..........YVMIDIVVAGWSALQYMREVTEGLAIHAHRAMHAAFTR...RHGITMLALAKAARMIGVDQIH..............IKRINDFLLS...........WEHIRPVFPVASGGLHPGLMPELIRLF.GKDLVIQAGGGVMGHPDGPRAGAKALRDAIDAAIEG..DLDEKA.SPELKKSLREV................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE]
2QYG-D  : .....GFYAK...........NYIELDFDFECA....PHEAAAHLCSEQSTA...........RPRFAAKVLELSA............RVTIAHPHGNF........AKIPNLLSAVCGEVFFSPGIPLIRLQDIRFPEPYLAAFDGPRFGIAGVRERLQAF....RPIFFGVIKPNIGLPPQPFAELGYQSWTGLDIAKDDEMLADVDWCPLAERAALLGDACRRASAETGVPKIYLANITDE.VDRLTELHDVAVAN..........ALLINAMPVGLSAVRMLRKHA.TVPLIAHFPFIAAFSR...NYGIHSRVMTRLQRLAGFDVVI..............VLDCIRACLE...........MGPIKPCLPVPGGSDSAATLENVYRKVGSADFGFVPGRGVFGHPMGPAAGATSIRQAWDAIAAG..PVPDHA.HPELAAALRAF................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE-LIKE PROTEIN 2]
2V67-A  : ....LTYYTPDYVV......DTDILAAFRMTPQ....PEECGAAVAAESST...........SLDRYKGRCYDIEP............IAYVAYXIDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFVGXPHGIQVERDKLNKY....RGLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTXDDENVNSQPFMRWRDRFLFVAEAIYKAQAETGEVKGHYLNATAGTCEEMMKRAVXAKEL..........IIMHDYLTGGFTANTSLAIYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHLH..............ILGFVDLMRDDYVE..YFTQDWXSMPGVMPVASGGIHVWHMPALVEIF.GDDACLQFGGGTLGHPWGNAPGAAANRVALEACTQ....IRSAC.SPELAAACEVW................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN]
3NWR-A  : ....................EDTLEADYLIET.....PARVADVMAGEQSSG............ARSRASVLRIEE............RITLSFPLANI.........NLPTLAATVAGNLYDLGEVTGVRLLSLRLPASYRARFELPRHGVAGTRALTDVK....RPMIGTIIKPNVGLSAAETAALVRELCEAVDFIXDDEVCANPAHAPLAERVRAVMSEVRRYRERSGRPVMVAFNITDD.LDAMRRHAELVERE..........CVMASINWCGFSAIQSLRRTT.PLVLHAHRNGYGMMSR...ALGMSFQAYQTLWRLSGVDHMH..............VIESARDCATP...............AVLPAFSSGQWAGTVQATFDAVRSTDLLFMSGGGILAHPDGPAAGVTSVRQAWAAVQAG..PLPVYA.MPELRRALAFF................... [: A RUBISCO-LIKE PROTEIN]
3QFW-B  : ......................RIVATYHIAS.....IEQRALALAIEQSVEC............NIVGRVEDVAE............AVRIGLAAATAP.......AEPGQLLNMLFGNSSIQPD...IALADVELPAHYLTAFGGPRVGLAGIRTLTGAQ....RALTASALKP.QGLSPAALASIAHQLALGVDLIKDDHGLADQAFSPFAERAAAVGKAVREANAARGGRTLYAPNISG.TLDDMRRQLGVIRDE..........AVLVAPMIVGVSNFHAIVKEAAGLVVVAHPAMAGAA........IAAPLLGRLFRLFGADATV..............CLALAQAARD...........FGKLNACIPTPAGGIMLQRVNELLRFYG.QDVMLLI..........LTEQASRFVNKVADYGQR....................................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE]
uniref90: ......................RIIATYHLAS.....VAERAKGLAIEQSVEC............TIVGRVEDIAE............AVRIGLAAATAP.......AEPGQLINMLFGNSSMQQD...VTLVDVELPPSYLAAFGGPRLGLAGLRALTGTQ....RALTASALKP.QGLSPAALARIAGQLARGVDVIKDDHGIADQAYSPFAARVEAVGRAVQEANVARDGHSLYAPNLSG.TLDDMRRQLDLAREQ..........AVMVAPMIVGLANFHAVVKAAAGMVVIAHPALSGVT........IAPPLLGKLFRLFGADATI..............CLQLARAGRD...........WGALEPCMPVPAGGLTADRVAELLQFYG.HDVMLLI..........LTEEAARFVNEVAAHGK........................................ [uniref90|Q07KC6 Ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit n=1 Tax=Rhodopseudomonas palustris BisA53 RepID=Q07KC6_RHOP5]
2ZVI-A  : ......................ELLATYLLT......TEKKAEQIATGLTVG...........MQKHKGRVIKVEE............VITIAYPEINFSQ.......DIPALLTTVFGKLSL...DGKIKLIDLHFSEAFKRALPGPKFGVYGIRKLLGE.....RPLLMSIFKGVIGRDLSDIKEQLRQQALGVDLIKDDEIFFETGLAPFETRIAEGKQILKETYEQTGHKTLYAVNLTGR.TADLKDKARRAAEL..........ALLFNVFAYGLDVMQGLAED..PVPIMAHPAVSGAFTS...FYGFSHALLGKLNRYCGADFSL..............ALAIHEECVR.............AFNQTFAVPSAGIHPGMVPLLMRDF.GIDHIINAGGGVHGHPNGAQGGGRAFRAIIDAVLEA..PIDEKA.CKDLKLALDKWGK................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE]
uniref90: ......................ELLATYVLT......DERKAEQIALGLTVG...........LQKHKGRVEKVTE............EVTIAYPEANFSA.......DIPAVLSTIFGKLSL...DGKVKLVDIQFSDRFKKSLPGPVFGIDGIRKKTGV.....RPLLMSIFKGVIGRDMTDLKEQLRLQALGVDFIKDDEILFESPLAPFEDRIKEGKKILKETYEETGHRTLYAVHLTGR.TFELRDRARKAAEL..........ALLFNVFAYGLDVMQSLAED..RLPIMAHPAVSGALTS...EYGFSHSLLGKLNRYAGADLSL..............AFGIYEACVK.............SVQKTFPVPSAGIHPGMVPVLMKDF.GLDHVINAGGGIHGHPRGAIGGGKAFRSIIDAVIHG..SIQEKT.CQDLKAALELWGR................. [uniref90|A8FCG8 2,3-diketo-5-methylthiopentyl-1-phosphate enolase n=2 Tax=Bacillus pumilus RepID=MTNW_BACP2]
2OEK-B  : ......................AVMATYLLHDE....IRKKAEGIALGLTIG...........LRKHKGEVVAIEE............IVKIAYPTVNFSA.......DLPALLVTTFGKLSLD...GEVRLLDLEFPDEWKRQFPGPRFGIDGIRDRVGVH....RPLLMSIFKGMIGRDLAYLTSELKKQALGVDLVXDDEILFDSELLPFEKRITEGKAALQEVYEQTGKRTLYAVNLTGK.TFALKDKAKRAAEL..........VLLFNVFAYGLDVLQALRED..AVPIMAHPAFSGAVTP...FYGVAPSLWGKLLRLAGADFVL..............ALGIARALTD.............PFARAFPVPSAGIHPGLVPLIIRDF.GLDTIVNAGGGIHGHPDGAIGGGRAFRAAIDAVLAG..PLRAAA.NEALQKAIDRWGV................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE ENOLASE]
uniref90: .......................IVASYYLRLE....PYEKAKSFAIGQSLG...........RKKYMGKIVNIVE............IFSIAYPFDNFGP.......KFPMIMTTLLGNASTS...TQAKLIDIYMPKKFTDMFNGPNFGIEGLREVSGVK....RPILLNMIKPCLGFKAEAGAEIFYQTALGVDLIKDDELLANPSYCTLEDRLDKYIEASNRAYEETGKKTLYVPNITDH.VDKILDNAKMAVDK..........LVMLNFASVGIDVLQYLTKN..DVPVIAHYASAGPYYE...FSGIASNLFGKFARMAGADVVM..............YLRTAHELML.............SYKK................................................................................................. [uniref90|F0H203 2,3-diketo-5-methylthiopentyl-1-phosphate enolase family protein n=2 Tax=Anaerococcus hydrogenalis RepID=F0H203_9FIRM]
3FK4-A  : ......................GIIATYLIHDD....LEKKAEQIALGLTIG...........LKQHKGNVIHVEE............IIKIEYPLLNFSP.......DLPAILTTTFGKLSLD...GEVKLIDLTFSDELKKHFPGPKFGIDGIRNLLQVH....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENALTPLTKRIVSGKEVLQSVYETYGHKTLYAVNLTGR.TFDLKENAKRAVQA..........ILLFNVFAYGLDVLQSLAED..PVPIMAHPAVSGAYSA...LYGVSSPLLGKLLRYAGADFSL..............ALAISKYLTE...........DASFKKSFSVPSAGIHPGFVPFIVRDF.GKDVVINAGGGIHGHPNGAQGGGKAFRTAIDATLQN..PLHEV..DINLHSALQIWG.................. [: RUBISCO-LIKE PROTEIN]
uniref90: ......................GITATYLIHDD....LNQKAEQIALGLTVG...........LKQHKGNVIHVEE............LIKIQYPSVNFSP.......DLPAILTTTFGKLSLD...GEVKLVDLTFSDDLKKHFPGPKFGIEGIRNLLHIQ....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENSLTPLTKRIHAGKEVLQSVYETYGHKTLYAVNLTGR.TYDLKENAKRAIEY..........ILLFNVFAYGLDVLQSLAED..SIPIMAHPAVSGAYAS...LYGFSYSLLGKLLRYAGADFSL..............ALLITHKLTE...........DPSLKRSFPVPSAGIHPGFVPFILRDF.GKNVVINAGGGIHGHPAGAQGGGKAFRAAIDATLQG..PLHEV..NVDLHAALQLWG.................. [uniref90|C2WBF2 2,3-diketo-5-methylthiopentyl-1-phosphate enolase n=4 Tax=Bacillus RepID=C2WBF2_BACCE]

NOTE: To save space, only 20 of 1109 template profile alignments are shown above. The complete set of alignments can be found in the file Homology_5hqm-~_profile.ali. The template profile contains structural alignments of 16 PDB files, which provide safe anchors for the remaining sequence-based alignments (only reliable regions shown).

In the alignment above, 452 of 470 target residues (96.2%) are aligned to template residues. Among these aligned residues, the sequence identity is 64.4% and the sequence similarity is 75.4% ('similar' means that the BLOSUM62 score is > 0). The following 5 loops had to be modeled (only the first of 2 similar loops in the homodimer is listed):

LoopN-terminal anchorLoop sequenceC-terminal anchor
1DPIEYAKTHKEFA
3LETFAKYNSASHV
5DCWKSGSDPIEYA
7KLIPAKGHGFLEV
9EIDETAFGDDPVKGGGLFKV

After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).

The resulting half-refined model has been saved as Homology_5hqm-~03_refined050.yob and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals0.108Optimal
Packing 1D-0.963Good
Packing 3D-1.361Satisfactory
Overall-0.993Good

Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as Homology_5hqm-~03_refined100.yob, the corresponding Z-scores are listed below:

Check typeQuality Z-scoreComment
Dihedrals0.456Optimal
Packing 1D-0.683Good
Packing 3D-1.425Satisfactory
Overall-0.863Good

Since the overall quality Z-score improved to -0.863 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.

The final model for this template and alignment has been saved as Homology_5hqm-~03.yob, and is shown below, together with a plot of its overall quality Z-score, shown per residue:

6.8. Homology model 8/15, based on template 5HAN-~, alignment variant 01

This model is a homodimer, and based on the following profile-profile alignment:

(To improve readability, only up to ten lines of the complete target multiple sequence alignment (MSA) shown above are also displayed here (upside down). The template MSA has been shrunk and focused on structurally aligned PDB entries. The actual target-template alignment can be found in the middle at the line named 'Match'.)

Q08EW6  : .......................................................................................................................NNQGGGDIEHAKIHGIYMPERAIQLFDGPSKDISDMWRILGRPVKDGGYNAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEIQGNQVFSPMNQTIPLVVDAMKRAQDETGQAKLFSANITADDQYEMCARADFILEAFGP..DADKVAFLVDGYVGDPGMITTARSQYPNQYLHYHRAGHGAVNSPKIKRGYTAFVLAKMSRLQGASGAHVGTMGYGKME................................................................................................................................ [uniref90|Q08EW6 Ribulose 1,5-bisphosphate carboxylase/oxygenase large subunit (Fragment) n=1 Tax=uncultured marine bacterium RepID=Q08EW6_9BACT]
Q5DVV5  : ............................................................................................................................................................................IIKPKLGLRPKPFAEACYNFWLGGDFIKNDEPQGNQIWGPIKEVVPLVKDSLVRAQDDTGMAKLFSFNITADDHYEMLHRGEYILETFAEFSE..NIAFLVDGCVGGPGMVTTARRNFPDQFLHYHRAGHGAVTSDQSDRGYNMLVHMKMARLQGASGIHTGTMGYGKMEGAADDKVIAYMLERDSADGLSYHQEWEGMKATTPIICGGMNA...................................................................................... [uniref90|Q5DVV5 Ribulose-1,5-bisphosphate carboxylase oxygenase large subunit (Fragment) n=11 Tax=uncultured prokaryote RepID=Q5DVV5_9ZZZZ]
Q933G7  : ........................................................................................................................................VPPAYLRLFDGPSTTIKDLWRVLGRPVVDGGFIVGTIIKPKLGLRPQPFADACYDFWLGGDFIKNDEPQGNQVFAPFKDTVRAVNDAMRRAQDATGQPKLFSFNITADDHYEMLARGEYILETFGE..NADHVAFLVDGYVAGPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHVGTMGYGKMEGEASDRDSAFMITQDSAEGPYFKQEW...................................................................................................... [uniref90|Q933G7 Form II ribulose 1,5-bisphosphate carboxylase/oxygenase (Fragment) n=5 Tax=Rhodopseudomonas palustris RepID=Q933G7_RHOPA]
F2ZCE9  : .....................................................................................................................................DFYVPPDFLRLFDGPATTISNLWRVLGRPHQNGGFIVGTIVKPKLGLRPRPFADACYDFWLGGDFIKNDEPQGNQTFSPLKETIPLVADAMRRAQDETGEAKLFSANITADDHYEMVARGEFILDTFGEF..ADHVAFLVDGYVAGAAAVTTARRSFPQQYLHYHRAGHGAITSPQSKRGYTAFVHCKMARLQGASGIHTGTMSFGKMEGEAADRAIAFMLEQDSADGPYFHQEWHGMNPTTSIISG.......................................................................................... [uniref90|F2ZCE9 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=1 Tax=uncultured bacterium RepID=F2ZCE9_9BACT]
F2ZCD0  : ......................................................................................................................GNNQGMGDIANAQMQDFYVPPAMLALFDGPAKSINDLWTLLGRDNENGGYIAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEPQGNQVFCPLKKVLPLVHDAMKRAQDETGEAKLFSLNITADDHYEMCARADFGLETFGE..DAPRLAFLVDGFVGGPGMVTTARRQYSSQYLHYHRAGHGMITSPSSKRGYTAYILAKMSRLMGASGIHVGTMGYGKMEGGADDKIIAYMIERDECQGPFYYQKWHGMKPTTPIVSGGM........................................................................................ [uniref90|F2ZCD0 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=4 Tax=uncultured bacterium RepID=F2ZCD0_9BACT]
F5BZE6  : ......................................................................................................................GNNQGMGDVEYAKMIDFYMARSLLTLFDGPAMNITDMWRVLGRPQVNGGMVVGTIIKPKLGLRPKPFADACYMFWMGGDFIKNDEPQGNQVFAPTREIIPLVAEAMERAQQETGEAKIFSANITADDPFEMIRRGEFILEAFGK..NASHVAFLVDGYVGGPSAVTLCRRYFPNQFLHYHRAGHGAVTSNQSKRGYTVLTHMKMSRLQGASGIHTGTMGYGKMEGDKNEKMVAYMIERDEAMGVYYNQPWHGMTATTPIISGGMNALR.................................................................................... [uniref90|F5BZE6 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II (Fragment) n=1 Tax=alpha proteobacterium LM-5 RepID=F5BZE6_9PROT]
Q9FPW1  : LDQSSRYADLSLDEATLVKNGKHVLVAYIMKPKAGYDYLATAAHFAAESSTGTNVNVCTTDDFTKSVDALVYYIDPDSEE.........MKIAYPTLLFDRNIIDGRGMMCSFLTLAIGNNQGMGDVEYGKIYDFYLPPSFLRLYDGPAVNVEDMWRILGKGTSNGGLVDGTIIKPKLGLQPNPFGEACYSFWQGGDFIKNDEPQGNQVFCQMNECIPEVVKAMRACVKETGSSKLFSANITADDPEEMIARGKYIMSQFGPLSE..NCAFLVDGYVAGGTAVTCCRRNFPKQFLHYHRAGHGSVTSPQTQRGYTAFVHTKISRVIGASGIHVGTMSFGKMEGDASDKNIAYMLQDDEADGPYYRQEWQGMKETTPIISGGMNALRLPAFFENLGHSNVILTAGGGSFGHKDGPKIGAISCRQGEEAWKSLSDVIEYAKTHEEIKGAFLTFQKDADQIYPGWKEKLG... [uniref90|Q9FPW1 Ribulose 1,5-bisphosphate carboxylase oxygenase large subunit n=1 Tax=Symbiodinium sp. RepID=Q9FPW1_SYMSP]
E6VVI6  : .DQTSRYVNFDLKEDQLIADGNHVLCAYIYKPANGYGNVEVAAHFAAESSTGTNVEVCTTDDFTKGVDALVYEVSDASNGDS......LMKIAYPVELFDRNIIDGRAMLASFLTLCIGNNQGMGDVAYAKMHDFYVPRQYLELFDGPSKNIADFWRMLGRPTENGGMIAGTIVKPKLGLRPKPFADACYHFWLGGDFVKNDEPQGNQVFAPLKETITAVADAMRRAQDETGEAKIFSANITADDPREMIARGEFILNAFGE..NASRVAFLVDGYVAGPTAITTARRNFPNQFLHYHRAGHGAVTSPQAKRGYTAFVLSKMSRLQGASGIHTGTMGFGKMEGEMADKSMAYMIEREEAQGPYFKQKWYGMKATTPMISGGMNALRLPGFFDNLGHSNICQTSGGGAFGHLDGPTAGALSLRQSHDAWIQGVNLLDYAKEHNELARAFESFPGDADRFYPTWRHQL.... [uniref90|E6VVI6 Ribulose-bisphosphate carboxylase n=1 Tax=Desulfovibrio aespoeensis Aspo-2 RepID=E6VVI6_DESAO]
Q8RTI1  : MDQSNRYADLSLKEDDLIKGGNHVLVAYLMKPKTGYGYLEAAAHFSAESSTGTNVEVSTTDDFTKGVDALVYEIDEAK.........EIMKIAYPVDLFDRNITDGRAMIVSFLTLAIGNNQGMGDIAYAKMLDFYVPQKYLRLFDGPSKDISDLWRILGRPVVNGGYIAGTIIKPKLGLRPKPFAEAAYQFWLGGDFIKNDEPQGNQVFSPMRETIPLVYDSMKRAMDETGEAKLFSANITADDHYEMMARGEFILNTFGP..DADKVAFLVDGYVGGPGMVTTARRHFANQYLHYHRAGHGAVTSPSAKRGYTAFVLAKMSRLQGASGIHVGTMGYGKMEGDATDKNIAYMIERDSADGPFYHQEWYGMKPTTPIISGGMNALRLPGFFENLGHANLINTSGGGSYGHIDSPAAGAISLRQAYECWQQGADPIEFAKEHKEFARAFESFPGDADTIFPGWREKLGVHK [uniref90|Q8RTI1 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II n=1 Tax=magnetite-containing magnetic vibrio RepID=Q8RTI1_9PROT]
Q0F2Z8  : MDQSNRYADLSLNEADLIAGGKHLLVAYKLIPAKGYGFLEVAAHIAAESSTGTNVEVSTTDDFTRGVDALVYDIDETAFGDEGVTGGGLMKVAYPVELFDPNLIDGHYNVSHMWSLILGNNQGMGDHEGLRMLDFMVPECMIRKFDGPSAGIADLWKVLGRPEVDGGYISGTIIKPKLGLRPEPFAKACLDFWLGGDFIKNDEPQANQPFCPMKVVIPKVAEAMDRAQQETGQAKLFSANATADYHGECVARGEYILSEFAKYGNEKHVAFLIDGFVTGPAGVTTARRAFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLARLQGASGIHTGTMGYGKMEGHGKETVLAYMLERDECMGHYFNQKWYGMKPTAPIISGGMNALRLPGFFENLGHGNVINTCGGGSFGHIDSPAAGGKSLDQAYDCWKSGTDPIEYAKTHGEFARAFESFPGDADKLYPGWRDKLGVHK [uniref90|Q0F2Z8 Ribulose-bisphosphate carboxylase n=1 Tax=Mariprofundus ferrooxydans PV-1 RepID=Q0F2Z8_9PROT]
SecStr  : CCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCEEECCCCCCHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCEEEECCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEECCCCCCHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCHHCCCCCCCEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHHHHCCCC [Secondary structure predicted by PsiPred]
Target  : MDQSNRYANLNLKEEDLIKNGKHLLVAYKLIPAKGHGFLEVAAHVAAESSTGTNVEVSTTDDFTRGVDALVYEIDETAFGDDPVKGGGLFKVAYPVELFDPNLTDGTYNISHMWSLILGNNQGMGDHQGLRMLDFLVPEMMVRKFDGPSANISNLWKVLGRSETDGGYIAGTIIKPKLGLRPEPFAKACYDFWLGGDFIKNDEPQANQPFCPMEVVMPKVAEAMDRAQQATGQAKLFSANITADYYKEMIHRGDFVLETFAKYNSASHVAFLVDGFVTGPAGVTTARREFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLVRLMGASGMHTGTMGYGKMEGHGKETVLAYMLERDECQGPYFYQKWYGMKATTPIISGGMNALRLPGFFQNLGHGNVINTCGGGAFGHIDSPAAGGISLGQAYDCWKSGSDPIEYAKTHKEFARAFESFPKDGDKLFAGWREKLGVHK
Match   : MDQSNRYANLNLKE:|LI :G|H:L AY | P    :F||:AAH AAESSTGTNVEV TTDDFTRGVDALVYE|DE:          :L:K|AYP|ELFD N: DG   I: : :L |GNNQGMGD |  |M DF VP   :| FDGPS::I::LW|VLGR   :GG|I:GTIIKPKLGLRP|PFA:ACYDFWLGGDFI:NDEPQ:NQ F:P:: ::  VA|AM RAQ: TG|AKLFS NITAD | EM| RG|F|LETFA   :A:H|AFLVDG|V:GPA:VTTARR FP  |LH|HRAGHGAVTS :S  G   :   K|:RL:GASG:HTGTMG|GKMEG:: | :|AYM| :D ::GPYF|Q:W GM: TTPIISGGMNALR|PGFF:NLGH:N:I T:GGGAFGH|D: AAG: SL QA :CWK:G:DP|E|AK H|EFARAFESFP:D:DKL| :WR KL    
Template: MDQSNRYANLNLKESELIAGGRHVLCAYIMKPK...NFIQTAAHFAAESSTGTNVEVFTTDDFTRGVDALVYEVDEA..........SLMKIAYPIELFDRNVIDGRAMIASFLTLTIGNNQGMGDVEYAKMYDFYVPPAYLKLFDGPSTTIKDLWRVLGRPVINGGFIVGTIIKPKLGLRPQPFANACYDFWLGGDFIXNDEPQGNQVFAPFKDTVRAVADAMRRAQDKTGEAKLFSFNITADDHYEMLARGEFILETFAD..NADHIAFLVDGYVAGPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHTGTMGFGKMEGEAADRAIAYMITEDAADGPYFHQEWLGMNPTTPIISGGMNALRMPGFFDNLGHSNLIMTAGGGAFGHVDGGAAGAKSLRQAEQCWKQGADPVEFAKDHREFARAFESFPQDADKLYPNWRAKL....
SecStr  : CCHHHHHCTTTTHHHHHHHHCCCEEEEEEEECC...HHHHHHHHHHHHHCCCCCCCTTTTHHHHHHCCCEEEEEETT..........EEEEEEETTTTCCCCCCCCCCCHHHHHHHHHGGGGCTTTTEEEEEEEEECHHHHHHCCCCCCCCHHHHHHHHHCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCEEEEETTTTCCTTTTHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCHHHHHHHHHHHHHHHHHC..TTTEEEEEEHHHHHCHHHHHHHHHHHCCCEEEEETTTTCCCCTTTTCCCCHHHHHHHHHHHHHCEEEEECTTTTCCCCCTTTTHHHHHHHHCEEEECCCEEEEETTTCCCEEEECCCCCCCHHHHHHHHHHCCCEEEEEHHHHHHCCCHHHHHHHHHHHHHHHHHHCCHHHHHHHCHHHHHHHHHHCHHHHHHHHCCTTTTC.... [Secondary structure assigned by YASARA]
1RSC-G  : ....LTYYTPDYTP.....KDTDLLAAFRFSPQ.....DEAGAAIAAESST..........TDMDRYKGKCYHIEP............FAFIAYPLDLFEE.......SVTNILTSIVGNVFGFKAIRSLRLEDIRFPVALVKTFQGPPHGIQVERDLLNKY....RPMLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKSQAETGEIKGHYLNVTAPTCEEMMKRAEFAKEL..........IIMHDFLTAGFTANTTLAKWCRGVLLHIHRAMHAVIDR...NHGIHFRVLAKCLRLSGGDHLH..............TLGFVDLMREDHIEA.FFTQDWASMPGVLPVASGGIHVWHMPALVEIF.GDDSVLQFGGGTLGHPWGNAPGATANRVALEACVQ...LREAGKWSPELAAALDLW................... [: RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (LARGE]
1GEH-B  : ..........GYEP.......RDIIAVFRVTPA.....EQAAGAVAAESST.GTWT..YEQERWADLSAKAYDFHD............IVRIAYPFHAFEE.......NLPGLLASIAGNIFGMKRVKGLRLEDLYFPEKLIREFDGPAFGIEGVRKMLEIK....RPIYGVVPKPKVGYSPEEFEKLAYDLLSNADYMKDDENLTSPWYNRFEERAEIMAKIIDKVENETGEKKTWFANITAD.LLEMEQRLEVLADL..........HAMVDVVITGWGALRYIRDLAAGLAIHGHRAMHAAFTR...YHGISMFVLAKLYRLIGIDQLH..............VIQNARILRESHYK...LEQKFYSIKAAFPTSSGGLHPGNIQPVIEAL.GTDIVLQLGGGTLGHPDGPAAGARAVRQAIDAIMQGIPLDEYAKTHKELARALEKW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE]
1SVD-A  : .....TYWMPEYTP.....LDSDILACFKITPQ.....EEAAAAVAAESSTG..........DMDYYKGRAYRIED............YAFIAYPIDLFEE.......SVVNVFTSLVGNVFGFKAVRGLRLEDVRFPLAYVKTCGGPPHGIQVERDKMNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFMRWRDRFLFVQDATETAEAQTGERKGHYLNVTAPTPEEMYKRAEFAKEI..........IIMHDYITGGFTANTGLAKWCQGVLLHIHRAMHAVIDR...NHGIHFRVLTKILRLSGGDHLH..............TLGWIDLLRESFIP..FFDQDWGSMPGVFAVASGGIHVWHMPALVNIF.GDDSVLQFGGGTLGHPWGNAAGAAANRVALEACVE...LTAAAQHSPELKIAMETW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE]
2YBV-A  : ......YYTPDYTP.....KDTDILAAFRVTPQ.....EEAAAAVAAESSTG........LTDLDRYKGCCYDIEP............IAYIAYPLDLFEE.......SVTNMLTSIVGNVFGFKALKALRLEDLRIPVAYLKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKAQAETGEIKGHYLNVTAPTCEEMLKRAEFAKEL..........IIMHDFLTAGFTANTTLSKWCRGMLLHIHRAMHAVMDR...NHGIHFRVLAKCLRMSGGDHIH..............TLGFVDLLRENYIE..YFTQDWASMPGVMAVASGGIHVWHMPALVDIF.GDDAVLQFG.....HPWGNAPGATANRVALEACIQ...IREAARWSPELAAAC...................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN]
1BXN-C  : ....MGYWDGDYVP.....KDTDLLALFRITPQ.....VEAAAAVAGESST..WTV......ACDMYRAKAYRVDP............FCYVAYDLSLFEE.......SIANLTASIIGNVFSFKPIKAARLEDMRFPVAYVKTFAGPSTGIIVERERLDKF....RPLLGATTKPKLGLSGRNYGRVVYEGLKGLDFMKDDENINSQPFMHWRDRFLFVMDAVNKASAATGEVKGSYLNVTAGTMEEMYRRAEFAKSL..........IIMVD.LIVGWTCIQSMSNWCRDMILHLHRAGHGTYTR...NHGVSFRVIAKWLRLAGVDHMH..............VQGYYNVCRDAYTQ..FFDQDWASLRKVMPVASGGIHAGQMHQLIHLF.GDDVVLQFGGGTIGHPQGIQAGATANRVALEAMVL...LRDAARWCGPLRAALDTW................... [: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)]
1EJ7-L  : .....TYYTPEYQT.....KDTDILAAFRVTPQ.....EEAGAAVAAESSTGTWTTV.....SLDRYKGRCYRIER............IAYVAYPLDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENVNSQPFMRWRDRFLFCAEALYKAQAETGEIKGHYLNATAGTCEEMIKRAVFAREL..........IVMHDYLTGGFTANTSLAHYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHIH..............TLGFVDLLRDDFVE..YFTQDWVSLPGVLPVASGGIHVWHMPALTEIF.GDDSVLQFGGGTLGHPWGNAPGAVANRVALEACVK...IREACKWSPELAAACEVW................... [: RUBISCO (LARGE SUBUNIT)]
1IWA-C  : ....MGYWNPDYQV.....KDTDVLALFRVTPQ.....IEAAAAVAGESST...........AADLYRAKAYKVDQ............FAYIAYELDLFEE.......SIANLTASIIGNVFGFKAVKALRLEDMRLPLAYLKTFQGPATGVILERERLDKF....RPLLGCTTKPKLGLSGKNYGRVVYEALKGLDFVKDDENINSQPFMRWRERYLFTMEAVNKASAATGEVKGHYLNVTAATMEEMYARANFAKEL..........IIMID.LVIGYTAIQTMAKWARDMILHLHRAGNSTYSR...NHGMNFRVICKWMRMAGVDHIH..............TRGFYKTLLLPKLE..FFDMEWASLRKVMPVASGGIHAGQMHQLIHYLG.EDVVLQFGGGTIGHPDGIQAGATANRVALEAMIL...LREAAKTCGALRTALDLW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE]
1TEL-B  : .....GFFAS...........QYLVLDYYLESV.....ETALAHFCSEQSTA........DEDFRVHAAKVIDYEV............RVTIAHPHCNFGP.......KIPNLLTAVCGETYFTPGVPVVKLMDIHFPDTYLADFEGPKFGIEGLRDILNAH....RPIFFGVVKPNIGLSPGEFAEIAYQSWLGLDIAKDDEMLADVTWSSIEERAAHLGKARRKAEAETGEPKIYLANITDE.VDSLMEKHDVAVRN..........ALLINALPVGLSAVRMLSNYT.QVPLIGHFPFIASFSR...KYGIHSKVMTKLQRLAGLDAVI..............VLENVIECTKP..........MGRIKPCLPVPGGSDSALTLQTVYEKVGNVDFGFVPGRGVFGHPMGPKAGAKSIRQAWEAIEQGISIETWAETHPELQAMVDQ.................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE, LARGE SUBUNIT]
2D69-A  : .....DFVDLNYEP.....GRDELIVEYYFEPN.....EEAAGRIASESSIGTW.........AKRSMAKVFYLEK............IAKIAYPLTLFEE.......SLVQLFSAVAGNVFGMKALKNLRLLDFHPPYEYLRHFKGPQFGVQGIREFMGVK....RPLTATVPKPKMGWSVEEYAEIAYELWSGIDLLKDDENFTSFPFNRFEERVRKLYRVRDRVEAETGETKEYLINITGP.VNIMEKRAEMVANE..........YVMIDIVVAGWSALQYMREVTEGLAIHAHRAMHAAFTR...RHGITMLALAKAARMIGVDQIH..............IKRINDFLLS...........WEHIRPVFPVASGGLHPGLMPELIRLF.GKDLVIQAGGGVMGHPDGPRAGAKALRDAIDAAIEGVDLDEKAKSSPELKKSLREV................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE]
2QYG-D  : .....GFYAK...........NYIELDFDFECA.....HEAAAHLCSEQSTA...........RPRFAAKVLELSA............RVTIAHPHGNF........AKIPNLLSAVCGEVFFSPGIPLIRLQDIRFPEPYLAAFDGPRFGIAGVRERLQAF....RPIFFGVIKPNIGLPPQPFAELGYQSWTGLDIAKDDEMLADVDWCPLAERAALLGDACRRASAETGVPKIYLANITDE.VDRLTELHDVAVAN..........ALLINAMPVGLSAVRMLRKHA.TVPLIAHFPFIAAFSR...NYGIHSRVMTRLQRLAGFDVVI..............VLDCIRACLE...........MGPIKPCLPVPGGSDSAATLENVYRKVGSADFGFVPGRGVFGHPMGPAAGATSIRQAWDAIAAGIPVPDHAASHPELAAALRAF................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE-LIKE PROTEIN 2]
2V67-A  : ....LTYYTPDYVV......DTDILAAFRMTPQ.....EECGAAVAAESST...........SLDRYKGRCYDIEP............IAYVAYXIDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFVGXPHGIQVERDKLNKY....RGLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTXDDENVNSQPFMRWRDRFLFVAEAIYKAQAETGEVKGHYLNATAGTCEEMMKRAVXAKEL..........IIMHDYLTGGFTANTSLAIYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHLH..............ILGFVDLMRDDYVE..YFTQDWXSMPGVMPVASGGIHVWHMPALVEIF.GDDACLQFGGGTLGHPWGNAPGAAANRVALEACTQ...IRSACKWSPELAAACEVW................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN]
3NWR-A  : ....................EDTLEADYLIET......ARVADVMAGEQSSG............ARSRASVLRIEE............RITLSFPLANI.........NLPTLAATVAGNLYDLGEVTGVRLLSLRLPASYRARFELPRHGVAGTRALTDVK....RPMIGTIIKPNVGLSAAETAALVRELCEAVDFIXDDEVCANPAHAPLAERVRAVMSEVRRYRERSGRPVMVAFNITDD.LDAMRRHAELVERE..........CVMASINWCGFSAIQSLRRTT.PLVLHAHRNGYGMMSR...ALGMSFQAYQTLWRLSGVDHMH..............VIESARDCATP...............AVLPAFSSGQWAGTVQATFDAVRSTDLLFMSGGGILAHPDGPAAGVTSVRQAWAAVQAGTPLPVYAEHMPELRRALAFF................... [: A RUBISCO-LIKE PROTEIN]
3QFW-B  : ......................RIVATYHIAS......EQRALALAIEQSVEC............NIVGRVEDVAE............AVRIGLAAATAP.......AEPGQLLNMLFGNSSIQPD...IALADVELPAHYLTAFGGPRVGLAGIRTLTGAQ....RALTASALKP.QGLSPAALASIAHQLALGVDLIKDDHGLADQAFSPFAERAAAVGKAVREANAARGGRTLYAPNISG.TLDDMRRQLGVIRDE..........AVLVAPMIVGVSNFHAIVKEAAGLVVVAHPAMAGAA........IAAPLLGRLFRLFGADATV..............CLALAQAARD...........FGKLNACIPTPAGGIMLQRVNELLRFYG.QDVMLLI..........LTEQASRFVNKVADYGQR....................................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE]
uniref90: ......................RIIVTYQVAA......AARAEALAIEQSVEC............EIVGRVEAIAP............SVRVSLASATAP.......AEPGQLLNMLFGNSSIQPD...VTLADVELPPAYPAAFGGPKLGISGLRAKLGAP....RALTGSALKP.QGLAPEALAGLAHRLALGVDLIKDDHGIADQAFSPFAARVPAVARAMREACAVRGAAMLYAPHVSG.SLDDMRRQLDIVRRE..........VVMLMPMIVGLANFHLIAKEAEGLIVLAHPSLAGAQ........IAPDLLGKLFRLLGADATI..............CRALADAARR...........WHDLKPCLPVPAGGIAIDRIKELLAFYG.TDVMLLI..........LTEHAARFTAEVASHGQ........................................ [uniref90|Q6N7T7 Ribulose bisphosphate carboxylase-like protein 1 n=2 Tax=Rhodopseudomonas palustris RepID=RBLL1_RHOPA]
2ZVI-A  : ......................ELLATYLLT.......EKKAEQIATGLTVG...........MQKHKGRVIKVEE............VITIAYPEINFSQ.......DIPALLTTVFGKLSL...DGKIKLIDLHFSEAFKRALPGPKFGVYGIRKLLGE.....RPLLMSIFKGVIGRDLSDIKEQLRQQALGVDLIKDDEIFFETGLAPFETRIAEGKQILKETYEQTGHKTLYAVNLTGR.TADLKDKARRAAEL..........ALLFNVFAYGLDVMQGLAED..PVPIMAHPAVSGAFTS...FYGFSHALLGKLNRYCGADFSL..............ALAIHEECVR.............AFNQTFAVPSAGIHPGMVPLLMRDF.GIDHIINAGGGVHGHPNGAQGGGRAFRAIIDAVLEAQPIDEKAEQCKDLKLALDKWGK................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE]
uniref90: ......................................HKQAKIIAVGQTAG...........LRQHLAEVIEIKT..............KIRFPEINVEN.......DLASLLTMIFGKYSM...AGAAKVIGVHLPESYGQR...PKFGITGIRKILNV.....RPLIMAIFKPALGLSAADHAVILKQVADALDIIKDDEILGDLETAPTLKRLEACRQVLEAIKQQTGRTVLYAVNVTGK.ADKLIEKARLLVKE..........ALLLNVLTYGFSVLEALAAD..NVPIFAHPAFAGAMCA...DTGLSYSVIGRFMAHGGVDAVL..............EKKIRDSLRS.............VF....PVPSAGIHPGIVPKAIADY.GDDVILNAGTGIMDHPNNPGAGVKAFFEALERVKTGQSFTLDTVPEGALKQALQKWG.................. [uniref90|B7KIK8 Ribulose-bisphosphate carboxylase n=1 Tax=Cyanothece sp. PCC 7424 RepID=B7KIK8_CYAP7]
2OEK-B  : ......................AVMATYLLHDE.....RKKAEGIALGLTIG...........LRKHKGEVVAIEE............IVKIAYPTVNFSA.......DLPALLVTTFGKLSLD...GEVRLLDLEFPDEWKRQFPGPRFGIDGIRDRVGVH....RPLLMSIFKGMIGRDLAYLTSELKKQALGVDLVXDDEILFDSELLPFEKRITEGKAALQEVYEQTGKRTLYAVNLTGK.TFALKDKAKRAAEL..........VLLFNVFAYGLDVLQALRED..AVPIMAHPAFSGAVTP...FYGVAPSLWGKLLRLAGADFVL..............ALGIARALTD.............PFARAFPVPSAGIHPGLVPLIIRDF.GLDTIVNAGGGIHGHPDGAIGGGRAFRAAIDAVLAGRPLRAAAAENEALQKAIDRWGV................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE ENOLASE]
uniref90: .......................VIATYRLAGG.....TKKAETIALGMTVG...........LQRHAGRVVSVDA............LIRIAYPLANLTP.......DLPSLLTATFGKLSMD...GKIRLLDLTLPPTFAAAFPGPKLGVEGIRERLGVH....RPLLMSIFKSCVGLTLAELAEGFFQQALGVDLIKDDEIFFNDTDAPFEQRLEACLQATERARRETGQTVLYAINLTGP.VHRLPEKARRAARL..........ALLINVLPYGFDLLQRLAED..TVPLIAHPALAGALYP...DYGIAAPLLGTLMRLAGADLVL..............ALGLASRLTD.............PHRPTFPVPSAGIHPGLVPHMMDDF.GLDVVINAGGGIHGHPGGAAAGGRAFRAAIAAGVGGVPLEQAAAGSRDLRAALDQWG.................. [uniref90|D5MLU6 2,3-diketo-5-methylthiopentyl-1-phosphate enolase (DK-MTP-1-P enolase) n=1 Tax=NC10 bacterium 'Dutch sediment' RepID=D5MLU6_9BACT]
3FK4-A  : ......................GIIATYLIHDD.....EKKAEQIALGLTIG...........LKQHKGNVIHVEE............IIKIEYPLLNFSP.......DLPAILTTTFGKLSLD...GEVKLIDLTFSDELKKHFPGPKFGIDGIRNLLQVH....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENALTPLTKRIVSGKEVLQSVYETYGHKTLYAVNLTGR.TFDLKENAKRAVQA..........ILLFNVFAYGLDVLQSLAED..PVPIMAHPAVSGAYSA...LYGVSSPLLGKLLRYAGADFSL..............ALAISKYLTE...........DASFKKSFSVPSAGIHPGFVPFIVRDF.GKDVVINAGGGIHGHPNGAQGGGKAFRTAIDATLQNKPLHEV..DDINLHSALQIWG.................. [: RUBISCO-LIKE PROTEIN]
uniref90: ......................GIIATYLIHDD.....EKKAEQIALGLTIG...........LKQHKGNVLHVEE............IIKIEYPLLNFSP.......DLPAILTTTFGKLSLD...GEVKLIDLTFSDELKKHFPGPKFGIDGIRNLLQVH....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENALTPLTNRIVSGKEVLQSVYETYGHKTLYAVNVTGR.TFDLKENAKRAVQA..........ILLFNVFAYGLDVLQSLAED..PVPIMAHPAVSGAYSA...LYGISSPLLGKLLRYAGADFSL..............ALAISKYLTE...........DVFFKKSFSVPSAGIHPGFVPFIIRDF.GKDVVINAGGGIHGHPNGAQGGGKAFRTAIDATLQNKPLHEV..DDINLHSALQIWG.................. [uniref90|C3P745 2,3-diketo-5-methylthiopentyl-1-phosphate enolase n=71 Tax=Bacillus cereus group RepID=MTNW_BACAA]

NOTE: To save space, only 20 of 1110 template profile alignments are shown above. The complete set of alignments can be found in the file Homology_5han-~_profile.ali. The template profile contains structural alignments of 16 PDB files, which provide safe anchors for the remaining sequence-based alignments (only reliable regions shown).

In the alignment above, 451 of 470 target residues (96.0%) are aligned to template residues. Among these aligned residues, the sequence identity is 65.0% and the sequence similarity is 76.7% ('similar' means that the BLOSUM62 score is > 0). The following 4 loops had to be modeled (only the first of 2 similar loops in the homodimer is listed):

LoopN-terminal anchorLoop sequenceC-terminal anchor
1LETFAKYNSASHV
3KLIPAKGHGFLEV
5EIDETAFGDDPVKGGGLFKV
7WREKLGVHKNone

After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).

The resulting half-refined model has been saved as Homology_5han-~01_refined050.yob and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals0.215Optimal
Packing 1D-0.766Good
Packing 3D-1.241Satisfactory
Overall-0.845Good

Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as Homology_5han-~01_refined100.yob, the corresponding Z-scores are listed below:

Check typeQuality Z-scoreComment
Dihedrals0.576Optimal
Packing 1D-0.390Good
Packing 3D-1.278Satisfactory
Overall-0.663Good

Since the overall quality Z-score improved to -0.663 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.

NOTE: 8 residues contained in N- and C-terminal unaligned tails of the homodimeric model have been excluded from the Z-scores in both tables above, since they are not reliable (YASARA does not yet perform ab initio structure prediction) and would have mainly added noise to the result.

The final model for this template and alignment has been saved as Homology_5han-~01.yob, and is shown below, together with a plot of its overall quality Z-score, shown per residue:

6.9. Homology model 9/15, based on template 5HAN-~, alignment variant 02

This model is a homodimer, and based on the following profile-profile alignment:

(To improve readability, only up to ten lines of the complete target multiple sequence alignment (MSA) shown above are also displayed here (upside down). The template MSA has been shrunk and focused on structurally aligned PDB entries. The actual target-template alignment can be found in the middle at the line named 'Match'.)

Q08EW6  : .......................................................................................................................NNQGGGDIEHAKIHGIYMPERAIQLFDGPSKDISDMWRILGRPVKDGGYNAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEIQGNQVFSPMNQTIPLVVDAMKRAQDETGQAKLFSANITADDQYEMCARADFILEAFGP..DADKVAFLVDGYVGDPGMITTARSQYPNQYLHYHRAGHGAVNSPKIKRGYTAFVLAKMSRLQGASGAHVGTMGYGKME................................................................................................................................ [uniref90|Q08EW6 Ribulose 1,5-bisphosphate carboxylase/oxygenase large subunit (Fragment) n=1 Tax=uncultured marine bacterium RepID=Q08EW6_9BACT]
Q5DVV5  : ............................................................................................................................................................................IIKPKLGLRPKPFAEACYNFWLGGDFIKNDEPQGNQIWGPIKEVVPLVKDSLVRAQDDTGMAKLFSFNITADDHYEMLHRGEYILETFAEFSE..NIAFLVDGCVGGPGMVTTARRNFPDQFLHYHRAGHGAVTSDQSDRGYNMLVHMKMARLQGASGIHTGTMGYGKMEGAADDKVIAYMLERDSADGLSYHQEWEGMKATTPIICGGMNA...................................................................................... [uniref90|Q5DVV5 Ribulose-1,5-bisphosphate carboxylase oxygenase large subunit (Fragment) n=11 Tax=uncultured prokaryote RepID=Q5DVV5_9ZZZZ]
Q933G7  : ........................................................................................................................................VPPAYLRLFDGPSTTIKDLWRVLGRPVVDGGFIVGTIIKPKLGLRPQPFADACYDFWLGGDFIKNDEPQGNQVFAPFKDTVRAVNDAMRRAQDATGQPKLFSFNITADDHYEMLARGEYILETFGE..NADHVAFLVDGYVAGPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHVGTMGYGKMEGEASDRDSAFMITQDSAEGPYFKQEW...................................................................................................... [uniref90|Q933G7 Form II ribulose 1,5-bisphosphate carboxylase/oxygenase (Fragment) n=5 Tax=Rhodopseudomonas palustris RepID=Q933G7_RHOPA]
F2ZCE9  : .....................................................................................................................................DFYVPPDFLRLFDGPATTISNLWRVLGRPHQNGGFIVGTIVKPKLGLRPRPFADACYDFWLGGDFIKNDEPQGNQTFSPLKETIPLVADAMRRAQDETGEAKLFSANITADDHYEMVARGEFILDTFGEF..ADHVAFLVDGYVAGAAAVTTARRSFPQQYLHYHRAGHGAITSPQSKRGYTAFVHCKMARLQGASGIHTGTMSFGKMEGEAADRAIAFMLEQDSADGPYFHQEWHGMNPTTSIISG.......................................................................................... [uniref90|F2ZCE9 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=1 Tax=uncultured bacterium RepID=F2ZCE9_9BACT]
F2ZCD0  : ......................................................................................................................GNNQGMGDIANAQMQDFYVPPAMLALFDGPAKSINDLWTLLGRDNENGGYIAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEPQGNQVFCPLKKVLPLVHDAMKRAQDETGEAKLFSLNITADDHYEMCARADFGLETFGE..DAPRLAFLVDGFVGGPGMVTTARRQYSSQYLHYHRAGHGMITSPSSKRGYTAYILAKMSRLMGASGIHVGTMGYGKMEGGADDKIIAYMIERDECQGPFYYQKWHGMKPTTPIVSGGM........................................................................................ [uniref90|F2ZCD0 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=4 Tax=uncultured bacterium RepID=F2ZCD0_9BACT]
F5BZE6  : ......................................................................................................................GNNQGMGDVEYAKMIDFYMARSLLTLFDGPAMNITDMWRVLGRPQVNGGMVVGTIIKPKLGLRPKPFADACYMFWMGGDFIKNDEPQGNQVFAPTREIIPLVAEAMERAQQETGEAKIFSANITADDPFEMIRRGEFILEAFGK..NASHVAFLVDGYVGGPSAVTLCRRYFPNQFLHYHRAGHGAVTSNQSKRGYTVLTHMKMSRLQGASGIHTGTMGYGKMEGDKNEKMVAYMIERDEAMGVYYNQPWHGMTATTPIISGGMNALR.................................................................................... [uniref90|F5BZE6 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II (Fragment) n=1 Tax=alpha proteobacterium LM-5 RepID=F5BZE6_9PROT]
Q9FPW1  : LDQSSRYADLSLDEATLVKNGKHVLVAYIMKPKAGYDYLATAAHFAAESSTGTNVNVCTTDDFTKSVDALVYYIDPDSEE.........MKIAYPTLLFDRNIIDGRGMMCSFLTLAIGNNQGMGDVEYGKIYDFYLPPSFLRLYDGPAVNVEDMWRILGKGTSNGGLVDGTIIKPKLGLQPNPFGEACYSFWQGGDFIKNDEPQGNQVFCQMNECIPEVVKAMRACVKETGSSKLFSANITADDPEEMIARGKYIMSQFGPLSE..NCAFLVDGYVAGGTAVTCCRRNFPKQFLHYHRAGHGSVTSPQTQRGYTAFVHTKISRVIGASGIHVGTMSFGKMEGDASDKNIAYMLQDDEADGPYYRQEWQGMKETTPIISGGMNALRLPAFFENLGHSNVILTAGGGSFGHKDGPKIGAISCRQGEEAWKSLSDVIEYAKTHEEIKGAFLTFQKDADQIYPGWKEKLG... [uniref90|Q9FPW1 Ribulose 1,5-bisphosphate carboxylase oxygenase large subunit n=1 Tax=Symbiodinium sp. RepID=Q9FPW1_SYMSP]
E6VVI6  : .DQTSRYVNFDLKEDQLIADGNHVLCAYIYKPANGYGNVEVAAHFAAESSTGTNVEVCTTDDFTKGVDALVYEVSDASNGDS......LMKIAYPVELFDRNIIDGRAMLASFLTLCIGNNQGMGDVAYAKMHDFYVPRQYLELFDGPSKNIADFWRMLGRPTENGGMIAGTIVKPKLGLRPKPFADACYHFWLGGDFVKNDEPQGNQVFAPLKETITAVADAMRRAQDETGEAKIFSANITADDPREMIARGEFILNAFGE..NASRVAFLVDGYVAGPTAITTARRNFPNQFLHYHRAGHGAVTSPQAKRGYTAFVLSKMSRLQGASGIHTGTMGFGKMEGEMADKSMAYMIEREEAQGPYFKQKWYGMKATTPMISGGMNALRLPGFFDNLGHSNICQTSGGGAFGHLDGPTAGALSLRQSHDAWIQGVNLLDYAKEHNELARAFESFPGDADRFYPTWRHQL.... [uniref90|E6VVI6 Ribulose-bisphosphate carboxylase n=1 Tax=Desulfovibrio aespoeensis Aspo-2 RepID=E6VVI6_DESAO]
Q8RTI1  : MDQSNRYADLSLKEDDLIKGGNHVLVAYLMKPKTGYGYLEAAAHFSAESSTGTNVEVSTTDDFTKGVDALVYEIDEAK.........EIMKIAYPVDLFDRNITDGRAMIVSFLTLAIGNNQGMGDIAYAKMLDFYVPQKYLRLFDGPSKDISDLWRILGRPVVNGGYIAGTIIKPKLGLRPKPFAEAAYQFWLGGDFIKNDEPQGNQVFSPMRETIPLVYDSMKRAMDETGEAKLFSANITADDHYEMMARGEFILNTFGP..DADKVAFLVDGYVGGPGMVTTARRHFANQYLHYHRAGHGAVTSPSAKRGYTAFVLAKMSRLQGASGIHVGTMGYGKMEGDATDKNIAYMIERDSADGPFYHQEWYGMKPTTPIISGGMNALRLPGFFENLGHANLINTSGGGSYGHIDSPAAGAISLRQAYECWQQGADPIEFAKEHKEFARAFESFPGDADTIFPGWREKLGVHK [uniref90|Q8RTI1 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II n=1 Tax=magnetite-containing magnetic vibrio RepID=Q8RTI1_9PROT]
Q0F2Z8  : MDQSNRYADLSLNEADLIAGGKHLLVAYKLIPAKGYGFLEVAAHIAAESSTGTNVEVSTTDDFTRGVDALVYDIDETAFGDEGVTGGGLMKVAYPVELFDPNLIDGHYNVSHMWSLILGNNQGMGDHEGLRMLDFMVPECMIRKFDGPSAGIADLWKVLGRPEVDGGYISGTIIKPKLGLRPEPFAKACLDFWLGGDFIKNDEPQANQPFCPMKVVIPKVAEAMDRAQQETGQAKLFSANATADYHGECVARGEYILSEFAKYGNEKHVAFLIDGFVTGPAGVTTARRAFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLARLQGASGIHTGTMGYGKMEGHGKETVLAYMLERDECMGHYFNQKWYGMKPTAPIISGGMNALRLPGFFENLGHGNVINTCGGGSFGHIDSPAAGGKSLDQAYDCWKSGTDPIEYAKTHGEFARAFESFPGDADKLYPGWRDKLGVHK [uniref90|Q0F2Z8 Ribulose-bisphosphate carboxylase n=1 Tax=Mariprofundus ferrooxydans PV-1 RepID=Q0F2Z8_9PROT]
SecStr  : CCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCEEECCCCCCHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCEEEECCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEECCCCCCHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCHHCCCCCCCEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHHHHCCCC [Secondary structure predicted by PsiPred]
Target  : MDQSNRYANLNLKEEDLIKNGKHLLVAYKLIPAKGHGFLEVAAHVAAESSTGTNVEVSTTDDFTRGVDALVYEIDETAFGDDPVKGGGLFKVAYPVELFDPNLTDGTYNISHMWSLILGNNQGMGDHQGLRMLDFLVPEMMVRKFDGPSANISNLWKVLGRSETDGGYIAGTIIKPKLGLRPEPFAKACYDFWLGGDFIKNDEPQANQPFCPMEVVMPKVAEAMDRAQQATGQAKLFSANITADYYKEMIHRGDFVLETFAKYNSASHVAFLVDGFVTGPAGVTTARREFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLVRLMGASGMHTGTMGYGKMEGHGKETVLAYMLERDECQGPYFYQKWYGMKATTPIISGGMNALRLPGFFQNLGHGNVINTCGGGAFGHIDSPAAGGISLGQAYDCWKSGSDPIEYAKTHKEFARAFESFPKDGDKLFAGWREKLGVHK
Match   : MDQSNRYANLNLKE:|LI :G|H:L AY | P    :F||:AAH AAESSTGTNVEV TTDDFTRGVDALVYE| | A         :L:K|AYP|ELFD N: DG   I: : :L |GNNQGMGD |  |M DF VP   :| FDGPS::I::LW|VLGR   :GG|I:GTIIKPKLGLRP|PFA:ACYDFWLGGDFI:NDEPQ:NQ F:P:: ::  VA|AM RAQ: TG|AKLFS NITAD | EM| RG|F|LETFA   :A:H|AFLVDG|V:GPA:VTTARR FP  |LH|HRAGHGAVTS :S  G   :   K|:RL:GASG:HTGTMG|GKMEG:: | :|AYM| :D ::GPYF|Q:W GM: TTPIISGGMNALR|PGFF:NLGH:N:I T:GGGAFGH|D: AAG: SL QA :CWK:G:DP|E|AK H|EFARAFESFP:D:DKL| :WR KL    
Template: MDQSNRYANLNLKESELIAGGRHVLCAYIMKPK...NFIQTAAHFAAESSTGTNVEVFTTDDFTRGVDALVYEV.DEAN........SLMKIAYPIELFDRNVIDGRAMIASFLTLTIGNNQGMGDVEYAKMYDFYVPPAYLKLFDGPSTTIKDLWRVLGRPVINGGFIVGTIIKPKLGLRPQPFANACYDFWLGGDFIXNDEPQGNQVFAPFKDTVRAVADAMRRAQDKTGEAKLFSFNITADDHYEMLARGEFILETFAD..NADHIAFLVDGYVAGPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHTGTMGFGKMEGEAADRAIAYMITEDAADGPYFHQEWLGMNPTTPIISGGMNALRMPGFFDNLGHSNLIMTAGGGAFGHVDGGAAGAKSLRQAEQCWKQGADPVEFAKDHREFARAFESFPQDADKLYPNWRAKL....
SecStr  : CCHHHHHCTTTTHHHHHHHHCCCEEEEEEEECC...HHHHHHHHHHHHHCCCCCCCTTTTHHHHHHCCCEEEEE.ETTT........EEEEEEETTTTCCCCCCCCCCCHHHHHHHHHGGGGCTTTTEEEEEEEEECHHHHHHCCCCCCCCHHHHHHHHHCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCEEEEETTTTCCTTTTHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCHHHHHHHHHHHHHHHHHC..TTTEEEEEEHHHHHCHHHHHHHHHHHCCCEEEEETTTTCCCCTTTTCCCCHHHHHHHHHHHHHCEEEEECTTTTCCCCCTTTTHHHHHHHHCEEEECCCEEEEETTTCCCEEEECCCCCCCHHHHHHHHHHCCCEEEEEHHHHHHCCCHHHHHHHHHHHHHHHHHHCCHHHHHHHCHHHHHHHHHHCHHHHHHHHCCTTTTC.... [Secondary structure assigned by YASARA]
1RSC-G  : ....LTYYTPDYTP.....KDTDLLAAFRFSPQ.....DEAGAAIAAESST..........TDMDRYKGKCYHI.EP...........FAFIAYPLDLFEE.......SVTNILTSIVGNVFGFKAIRSLRLEDIRFPVALVKTFQGPPHGIQVERDLLNKY....RPMLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKSQAETGEIKGHYLNVTAPTCEEMMKRAEFAKEL..........IIMHDFLTAGFTANTTLAKWCRGVLLHIHRAMHAVIDR...NHGIHFRVLAKCLRLSGGDHLH..............TLGFVDLMREDHIEA.FFTQDWASMPGVLPVASGGIHVWHMPALVEIF.GDDSVLQFGGGTLGHPWGNAPGATANRVALEACVQ...LREAGKWSPELAAALDLW................... [: RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (LARGE]
1GEH-B  : ..........GYEP.......RDIIAVFRVTPA.....EQAAGAVAAESST.GTWT..YEQERWADLSAKAYDF.HD...........IVRIAYPFHAFEE.......NLPGLLASIAGNIFGMKRVKGLRLEDLYFPEKLIREFDGPAFGIEGVRKMLEIK....RPIYGVVPKPKVGYSPEEFEKLAYDLLSNADYMKDDENLTSPWYNRFEERAEIMAKIIDKVENETGEKKTWFANITAD.LLEMEQRLEVLADL..........HAMVDVVITGWGALRYIRDLAAGLAIHGHRAMHAAFTR...YHGISMFVLAKLYRLIGIDQLH..............VIQNARILRESHYK...LEQKFYSIKAAFPTSSGGLHPGNIQPVIEAL.GTDIVLQLGGGTLGHPDGPAAGARAVRQAIDAIMQGIPLDEYAKTHKELARALEKW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE]
1SVD-A  : .....TYWMPEYTP.....LDSDILACFKITPQ.....EEAAAAVAAESSTG..........DMDYYKGRAYRI.ED...........YAFIAYPIDLFEE.......SVVNVFTSLVGNVFGFKAVRGLRLEDVRFPLAYVKTCGGPPHGIQVERDKMNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFMRWRDRFLFVQDATETAEAQTGERKGHYLNVTAPTPEEMYKRAEFAKEI..........IIMHDYITGGFTANTGLAKWCQGVLLHIHRAMHAVIDR...NHGIHFRVLTKILRLSGGDHLH..............TLGWIDLLRESFIP..FFDQDWGSMPGVFAVASGGIHVWHMPALVNIF.GDDSVLQFGGGTLGHPWGNAAGAAANRVALEACVE...LTAAAQHSPELKIAMETW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE]
2YBV-A  : ......YYTPDYTP.....KDTDILAAFRVTPQ.....EEAAAAVAAESSTG........LTDLDRYKGCCYDI.EP...........IAYIAYPLDLFEE.......SVTNMLTSIVGNVFGFKALKALRLEDLRIPVAYLKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKAQAETGEIKGHYLNVTAPTCEEMLKRAEFAKEL..........IIMHDFLTAGFTANTTLSKWCRGMLLHIHRAMHAVMDR...NHGIHFRVLAKCLRMSGGDHIH..............TLGFVDLLRENYIE..YFTQDWASMPGVMAVASGGIHVWHMPALVDIF.GDDAVLQFG.....HPWGNAPGATANRVALEACIQ...IREAARWSPELAAAC...................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN]
1BXN-C  : ....MGYWDGDYVP.....KDTDLLALFRITPQ.....VEAAAAVAGESST..WTV......ACDMYRAKAYRV.DP...........FCYVAYDLSLFEE.......SIANLTASIIGNVFSFKPIKAARLEDMRFPVAYVKTFAGPSTGIIVERERLDKF....RPLLGATTKPKLGLSGRNYGRVVYEGLKGLDFMKDDENINSQPFMHWRDRFLFVMDAVNKASAATGEVKGSYLNVTAGTMEEMYRRAEFAKSL..........IIMVD.LIVGWTCIQSMSNWCRDMILHLHRAGHGTYTR...NHGVSFRVIAKWLRLAGVDHMH..............VQGYYNVCRDAYTQ..FFDQDWASLRKVMPVASGGIHAGQMHQLIHLF.GDDVVLQFGGGTIGHPQGIQAGATANRVALEAMVL...LRDAARWCGPLRAALDTW................... [: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)]
1EJ7-L  : .....TYYTPEYQT.....KDTDILAAFRVTPQ.....EEAGAAVAAESSTGTWTTV.....SLDRYKGRCYRI.ER...........IAYVAYPLDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENVNSQPFMRWRDRFLFCAEALYKAQAETGEIKGHYLNATAGTCEEMIKRAVFAREL..........IVMHDYLTGGFTANTSLAHYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHIH..............TLGFVDLLRDDFVE..YFTQDWVSLPGVLPVASGGIHVWHMPALTEIF.GDDSVLQFGGGTLGHPWGNAPGAVANRVALEACVK...IREACKWSPELAAACEVW................... [: RUBISCO (LARGE SUBUNIT)]
1IWA-C  : ....MGYWNPDYQV.....KDTDVLALFRVTPQ.....IEAAAAVAGESST...........AADLYRAKAYKV.DQ...........FAYIAYELDLFEE.......SIANLTASIIGNVFGFKAVKALRLEDMRLPLAYLKTFQGPATGVILERERLDKF....RPLLGCTTKPKLGLSGKNYGRVVYEALKGLDFVKDDENINSQPFMRWRERYLFTMEAVNKASAATGEVKGHYLNVTAATMEEMYARANFAKEL..........IIMID.LVIGYTAIQTMAKWARDMILHLHRAGNSTYSR...NHGMNFRVICKWMRMAGVDHIH..............TRGFYKTLLLPKLE..FFDMEWASLRKVMPVASGGIHAGQMHQLIHYLG.EDVVLQFGGGTIGHPDGIQAGATANRVALEAMIL...LREAAKTCGALRTALDLW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE]
1TEL-B  : .....GFFAS...........QYLVLDYYLESV.....ETALAHFCSEQSTA........DEDFRVHAAKVIDY.EV...........RVTIAHPHCNFGP.......KIPNLLTAVCGETYFTPGVPVVKLMDIHFPDTYLADFEGPKFGIEGLRDILNAH....RPIFFGVVKPNIGLSPGEFAEIAYQSWLGLDIAKDDEMLADVTWSSIEERAAHLGKARRKAEAETGEPKIYLANITDE.VDSLMEKHDVAVRN..........ALLINALPVGLSAVRMLSNYT.QVPLIGHFPFIASFSR...KYGIHSKVMTKLQRLAGLDAVI..............VLENVIECTKP..........MGRIKPCLPVPGGSDSALTLQTVYEKVGNVDFGFVPGRGVFGHPMGPKAGAKSIRQAWEAIEQGISIETWAETHPELQAMVDQ.................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE, LARGE SUBUNIT]
2D69-A  : .....DFVDLNYEP.....GRDELIVEYYFEPN.....EEAAGRIASESSIGTW.........AKRSMAKVFYL.EK...........IAKIAYPLTLFEE.......SLVQLFSAVAGNVFGMKALKNLRLLDFHPPYEYLRHFKGPQFGVQGIREFMGVK....RPLTATVPKPKMGWSVEEYAEIAYELWSGIDLLKDDENFTSFPFNRFEERVRKLYRVRDRVEAETGETKEYLINITGP.VNIMEKRAEMVANE..........YVMIDIVVAGWSALQYMREVTEGLAIHAHRAMHAAFTR...RHGITMLALAKAARMIGVDQIH..............IKRINDFLLS...........WEHIRPVFPVASGGLHPGLMPELIRLF.GKDLVIQAGGGVMGHPDGPRAGAKALRDAIDAAIEGVDLDEKAKSSPELKKSLREV................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE]
2QYG-D  : .....GFYAK...........NYIELDFDFECA.....HEAAAHLCSEQSTA...........RPRFAAKVLEL.SA...........RVTIAHPHGNF........AKIPNLLSAVCGEVFFSPGIPLIRLQDIRFPEPYLAAFDGPRFGIAGVRERLQAF....RPIFFGVIKPNIGLPPQPFAELGYQSWTGLDIAKDDEMLADVDWCPLAERAALLGDACRRASAETGVPKIYLANITDE.VDRLTELHDVAVAN..........ALLINAMPVGLSAVRMLRKHA.TVPLIAHFPFIAAFSR...NYGIHSRVMTRLQRLAGFDVVI..............VLDCIRACLE...........MGPIKPCLPVPGGSDSAATLENVYRKVGSADFGFVPGRGVFGHPMGPAAGATSIRQAWDAIAAGIPVPDHAASHPELAAALRAF................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE-LIKE PROTEIN 2]
2V67-A  : ....LTYYTPDYVV......DTDILAAFRMTPQ.....EECGAAVAAESST...........SLDRYKGRCYDI.EP...........IAYVAYXIDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFVGXPHGIQVERDKLNKY....RGLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTXDDENVNSQPFMRWRDRFLFVAEAIYKAQAETGEVKGHYLNATAGTCEEMMKRAVXAKEL..........IIMHDYLTGGFTANTSLAIYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHLH..............ILGFVDLMRDDYVE..YFTQDWXSMPGVMPVASGGIHVWHMPALVEIF.GDDACLQFGGGTLGHPWGNAPGAAANRVALEACTQ...IRSACKWSPELAAACEVW................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN]
3NWR-A  : ....................EDTLEADYLIET......ARVADVMAGEQSSG............ARSRASVLRI.EE...........RITLSFPLANI.........NLPTLAATVAGNLYDLGEVTGVRLLSLRLPASYRARFELPRHGVAGTRALTDVK....RPMIGTIIKPNVGLSAAETAALVRELCEAVDFIXDDEVCANPAHAPLAERVRAVMSEVRRYRERSGRPVMVAFNITDD.LDAMRRHAELVERE..........CVMASINWCGFSAIQSLRRTT.PLVLHAHRNGYGMMSR...ALGMSFQAYQTLWRLSGVDHMH..............VIESARDCATP...............AVLPAFSSGQWAGTVQATFDAVRSTDLLFMSGGGILAHPDGPAAGVTSVRQAWAAVQAGTPLPVYAEHMPELRRALAFF................... [: A RUBISCO-LIKE PROTEIN]
3QFW-B  : ......................RIVATYHIAS......EQRALALAIEQSVEC............NIVGRVEDV.AE...........AVRIGLAAATAP.......AEPGQLLNMLFGNSSIQPD...IALADVELPAHYLTAFGGPRVGLAGIRTLTGAQ....RALTASALKP.QGLSPAALASIAHQLALGVDLIKDDHGLADQAFSPFAERAAAVGKAVREANAARGGRTLYAPNISG.TLDDMRRQLGVIRDE..........AVLVAPMIVGVSNFHAIVKEAAGLVVVAHPAMAGAA........IAAPLLGRLFRLFGADATV..............CLALAQAARD...........FGKLNACIPTPAGGIMLQRVNELLRFYG.QDVMLLI..........LTEQASRFVNKVADYGQR....................................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE]
uniref90: ......................RIIVTYQVAA......AARAEALAIEQSVEC............EIVGRVEAI.AP...........SVRVSLASATAP.......AEPGQLLNMLFGNSSIQPD...VTLADVELPPAYPAAFGGPKLGISGLRAKLGAP....RALTGSALKP.QGLAPEALAGLAHRLALGVDLIKDDHGIADQAFSPFAARVPAVARAMREACAVRGAAMLYAPHVSG.SLDDMRRQLDIVRRE..........VVMLMPMIVGLANFHLIAKEAEGLIVLAHPSLAGAQ........IAPDLLGKLFRLLGADATI..............CRALADAARR...........WHDLKPCLPVPAGGIAIDRIKELLAFYG.TDVMLLI..........LTEHAARFTAEVASHGQ........................................ [uniref90|Q6N7T7 Ribulose bisphosphate carboxylase-like protein 1 n=2 Tax=Rhodopseudomonas palustris RepID=RBLL1_RHOPA]
2ZVI-A  : ......................ELLATYLLT.......EKKAEQIATGLTVG...........MQKHKGRVIKV.EE...........VITIAYPEINFSQ.......DIPALLTTVFGKLSL...DGKIKLIDLHFSEAFKRALPGPKFGVYGIRKLLGE.....RPLLMSIFKGVIGRDLSDIKEQLRQQALGVDLIKDDEIFFETGLAPFETRIAEGKQILKETYEQTGHKTLYAVNLTGR.TADLKDKARRAAEL..........ALLFNVFAYGLDVMQGLAED..PVPIMAHPAVSGAFTS...FYGFSHALLGKLNRYCGADFSL..............ALAIHEECVR.............AFNQTFAVPSAGIHPGMVPLLMRDF.GIDHIINAGGGVHGHPNGAQGGGRAFRAIIDAVLEAQPIDEKAEQCKDLKLALDKWGK................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE]
uniref90: ......................................HKQAKIIAVGQTAG...........LRQHLAEVIEI.KT.............KIRFPEINVEN.......DLASLLTMIFGKYSM...AGAAKVIGVHLPESYGQR...PKFGITGIRKILNV.....RPLIMAIFKPALGLSAADHAVILKQVADALDIIKDDEILGDLETAPTLKRLEACRQVLEAIKQQTGRTVLYAVNVTGK.ADKLIEKARLLVKE..........ALLLNVLTYGFSVLEALAAD..NVPIFAHPAFAGAMCA...DTGLSYSVIGRFMAHGGVDAVL..............EKKIRDSLRS.............VF....PVPSAGIHPGIVPKAIADY.GDDVILNAGTGIMDHPNNPGAGVKAFFEALERVKTGQSFTLDTVPEGALKQALQKWG.................. [uniref90|B7KIK8 Ribulose-bisphosphate carboxylase n=1 Tax=Cyanothece sp. PCC 7424 RepID=B7KIK8_CYAP7]
2OEK-B  : ......................AVMATYLLHDE.....RKKAEGIALGLTIG...........LRKHKGEVVAI.EE...........IVKIAYPTVNFSA.......DLPALLVTTFGKLSLD...GEVRLLDLEFPDEWKRQFPGPRFGIDGIRDRVGVH....RPLLMSIFKGMIGRDLAYLTSELKKQALGVDLVXDDEILFDSELLPFEKRITEGKAALQEVYEQTGKRTLYAVNLTGK.TFALKDKAKRAAEL..........VLLFNVFAYGLDVLQALRED..AVPIMAHPAFSGAVTP...FYGVAPSLWGKLLRLAGADFVL..............ALGIARALTD.............PFARAFPVPSAGIHPGLVPLIIRDF.GLDTIVNAGGGIHGHPDGAIGGGRAFRAAIDAVLAGRPLRAAAAENEALQKAIDRWGV................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE ENOLASE]
uniref90: .......................VIATYRLAGG.....TKKAETIALGMTVG...........LQRHAGRVVSV.DA...........LIRIAYPLANLTP.......DLPSLLTATFGKLSMD...GKIRLLDLTLPPTFAAAFPGPKLGVEGIRERLGVH....RPLLMSIFKSCVGLTLAELAEGFFQQALGVDLIKDDEIFFNDTDAPFEQRLEACLQATERARRETGQTVLYAINLTGP.VHRLPEKARRAARL..........ALLINVLPYGFDLLQRLAED..TVPLIAHPALAGALYP...DYGIAAPLLGTLMRLAGADLVL..............ALGLASRLTD.............PHRPTFPVPSAGIHPGLVPHMMDDF.GLDVVINAGGGIHGHPGGAAAGGRAFRAAIAAGVGGVPLEQAAAGSRDLRAALDQWG.................. [uniref90|D5MLU6 2,3-diketo-5-methylthiopentyl-1-phosphate enolase (DK-MTP-1-P enolase) n=1 Tax=NC10 bacterium 'Dutch sediment' RepID=D5MLU6_9BACT]
3FK4-A  : ......................GIIATYLIHDD.....EKKAEQIALGLTIG...........LKQHKGNVIHV.EE...........IIKIEYPLLNFSP.......DLPAILTTTFGKLSLD...GEVKLIDLTFSDELKKHFPGPKFGIDGIRNLLQVH....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENALTPLTKRIVSGKEVLQSVYETYGHKTLYAVNLTGR.TFDLKENAKRAVQA..........ILLFNVFAYGLDVLQSLAED..PVPIMAHPAVSGAYSA...LYGVSSPLLGKLLRYAGADFSL..............ALAISKYLTE...........DASFKKSFSVPSAGIHPGFVPFIVRDF.GKDVVINAGGGIHGHPNGAQGGGKAFRTAIDATLQNKPLHEV..DDINLHSALQIWG.................. [: RUBISCO-LIKE PROTEIN]
uniref90: ......................GIIATYLIHDD.....EKKAEQIALGLTIG...........LKQHKGNVLHV.EE...........IIKIEYPLLNFSP.......DLPAILTTTFGKLSLD...GEVKLIDLTFSDELKKHFPGPKFGIDGIRNLLQVH....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENALTPLTNRIVSGKEVLQSVYETYGHKTLYAVNVTGR.TFDLKENAKRAVQA..........ILLFNVFAYGLDVLQSLAED..PVPIMAHPAVSGAYSA...LYGISSPLLGKLLRYAGADFSL..............ALAISKYLTE...........DVFFKKSFSVPSAGIHPGFVPFIIRDF.GKDVVINAGGGIHGHPNGAQGGGKAFRTAIDATLQNKPLHEV..DDINLHSALQIWG.................. [uniref90|C3P745 2,3-diketo-5-methylthiopentyl-1-phosphate enolase n=71 Tax=Bacillus cereus group RepID=MTNW_BACAA]

NOTE: To save space, only 20 of 1110 template profile alignments are shown above. The complete set of alignments can be found in the file Homology_5han-~_profile.ali. The template profile contains structural alignments of 16 PDB files, which provide safe anchors for the remaining sequence-based alignments (only reliable regions shown).

In the alignment above, 452 of 470 target residues (96.2%) are aligned to template residues. Among these aligned residues, the sequence identity is 64.6% and the sequence similarity is 76.5% ('similar' means that the BLOSUM62 score is > 0). The following 5 loops had to be modeled (only the first of 2 similar loops in the homodimer is listed):

LoopN-terminal anchorLoop sequenceC-terminal anchor
1LVYEIDETAFGDD
3LETFAKYNSASHV
5KLIPAKGHGFLEV
7DETAFGDDPVKGGGLFKV
9WREKLGVHKNone

After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).

The resulting half-refined model has been saved as Homology_5han-~02_refined050.yob and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals0.232Optimal
Packing 1D-0.810Good
Packing 3D-1.302Satisfactory
Overall-0.887Good

Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as Homology_5han-~02_refined100.yob, the corresponding Z-scores are listed below:

Check typeQuality Z-scoreComment
Dihedrals0.434Optimal
Packing 1D-0.412Good
Packing 3D-1.356Satisfactory
Overall-0.728Good

Since the overall quality Z-score improved to -0.728 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.

NOTE: 8 residues contained in N- and C-terminal unaligned tails of the homodimeric model have been excluded from the Z-scores in both tables above, since they are not reliable (YASARA does not yet perform ab initio structure prediction) and would have mainly added noise to the result.

The final model for this template and alignment has been saved as Homology_5han-~02.yob, and is shown below, together with a plot of its overall quality Z-score, shown per residue:

6.10. Homology model 10/15, based on template 5HAN-~, alignment variant 03

This model is a homodimer, and based on the following profile-profile alignment:

(To improve readability, only up to ten lines of the complete target multiple sequence alignment (MSA) shown above are also displayed here (upside down). The template MSA has been shrunk and focused on structurally aligned PDB entries. The actual target-template alignment can be found in the middle at the line named 'Match'.)

Q08EW6  : .......................................................................................................................NNQGGGDIEHAKIHGIYMPERAIQLFDGPSKDISDMWRILGRPVKDGGYNAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEIQGNQVFSPMNQTIPLVVDAMKRAQDETGQAKLFSANITADDQYEMCARADFILEAFGP..DADKVAFLVDGYVGDPGMITTARSQYPNQYLHYHRAGHGAVNSPKIKRGYTAFVLAKMSRLQGASGAHVGTMGYGKME................................................................................................................................ [uniref90|Q08EW6 Ribulose 1,5-bisphosphate carboxylase/oxygenase large subunit (Fragment) n=1 Tax=uncultured marine bacterium RepID=Q08EW6_9BACT]
Q5DVV5  : ............................................................................................................................................................................IIKPKLGLRPKPFAEACYNFWLGGDFIKNDEPQGNQIWGPIKEVVPLVKDSLVRAQDDTGMAKLFSFNITADDHYEMLHRGEYILETFAEFSE..NIAFLVDGCVGGPGMVTTARRNFPDQFLHYHRAGHGAVTSDQSDRGYNMLVHMKMARLQGASGIHTGTMGYGKMEGAADDKVIAYMLERDSADGLSYHQEWEGMKATTPIICGGMNA...................................................................................... [uniref90|Q5DVV5 Ribulose-1,5-bisphosphate carboxylase oxygenase large subunit (Fragment) n=11 Tax=uncultured prokaryote RepID=Q5DVV5_9ZZZZ]
Q933G7  : ........................................................................................................................................VPPAYLRLFDGPSTTIKDLWRVLGRPVVDGGFIVGTIIKPKLGLRPQPFADACYDFWLGGDFIKNDEPQGNQVFAPFKDTVRAVNDAMRRAQDATGQPKLFSFNITADDHYEMLARGEYILETFGE..NADHVAFLVDGYVAGPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHVGTMGYGKMEGEASDRDSAFMITQDSAEGPYFKQEW...................................................................................................... [uniref90|Q933G7 Form II ribulose 1,5-bisphosphate carboxylase/oxygenase (Fragment) n=5 Tax=Rhodopseudomonas palustris RepID=Q933G7_RHOPA]
F2ZCE9  : .....................................................................................................................................DFYVPPDFLRLFDGPATTISNLWRVLGRPHQNGGFIVGTIVKPKLGLRPRPFADACYDFWLGGDFIKNDEPQGNQTFSPLKETIPLVADAMRRAQDETGEAKLFSANITADDHYEMVARGEFILDTFGEF..ADHVAFLVDGYVAGAAAVTTARRSFPQQYLHYHRAGHGAITSPQSKRGYTAFVHCKMARLQGASGIHTGTMSFGKMEGEAADRAIAFMLEQDSADGPYFHQEWHGMNPTTSIISG.......................................................................................... [uniref90|F2ZCE9 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=1 Tax=uncultured bacterium RepID=F2ZCE9_9BACT]
F2ZCD0  : ......................................................................................................................GNNQGMGDIANAQMQDFYVPPAMLALFDGPAKSINDLWTLLGRDNENGGYIAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEPQGNQVFCPLKKVLPLVHDAMKRAQDETGEAKLFSLNITADDHYEMCARADFGLETFGE..DAPRLAFLVDGFVGGPGMVTTARRQYSSQYLHYHRAGHGMITSPSSKRGYTAYILAKMSRLMGASGIHVGTMGYGKMEGGADDKIIAYMIERDECQGPFYYQKWHGMKPTTPIVSGGM........................................................................................ [uniref90|F2ZCD0 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=4 Tax=uncultured bacterium RepID=F2ZCD0_9BACT]
F5BZE6  : ......................................................................................................................GNNQGMGDVEYAKMIDFYMARSLLTLFDGPAMNITDMWRVLGRPQVNGGMVVGTIIKPKLGLRPKPFADACYMFWMGGDFIKNDEPQGNQVFAPTREIIPLVAEAMERAQQETGEAKIFSANITADDPFEMIRRGEFILEAFGK..NASHVAFLVDGYVGGPSAVTLCRRYFPNQFLHYHRAGHGAVTSNQSKRGYTVLTHMKMSRLQGASGIHTGTMGYGKMEGDKNEKMVAYMIERDEAMGVYYNQPWHGMTATTPIISGGMNALR.................................................................................... [uniref90|F5BZE6 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II (Fragment) n=1 Tax=alpha proteobacterium LM-5 RepID=F5BZE6_9PROT]
Q9FPW1  : LDQSSRYADLSLDEATLVKNGKHVLVAYIMKPKAGYDYLATAAHFAAESSTGTNVNVCTTDDFTKSVDALVYYIDPDSEE.........MKIAYPTLLFDRNIIDGRGMMCSFLTLAIGNNQGMGDVEYGKIYDFYLPPSFLRLYDGPAVNVEDMWRILGKGTSNGGLVDGTIIKPKLGLQPNPFGEACYSFWQGGDFIKNDEPQGNQVFCQMNECIPEVVKAMRACVKETGSSKLFSANITADDPEEMIARGKYIMSQFGPLSE..NCAFLVDGYVAGGTAVTCCRRNFPKQFLHYHRAGHGSVTSPQTQRGYTAFVHTKISRVIGASGIHVGTMSFGKMEGDASDKNIAYMLQDDEADGPYYRQEWQGMKETTPIISGGMNALRLPAFFENLGHSNVILTAGGGSFGHKDGPKIGAISCRQGEEAWKSLSDVIEYAKTHEEIKGAFLTFQKDADQIYPGWKEKLG... [uniref90|Q9FPW1 Ribulose 1,5-bisphosphate carboxylase oxygenase large subunit n=1 Tax=Symbiodinium sp. RepID=Q9FPW1_SYMSP]
E6VVI6  : .DQTSRYVNFDLKEDQLIADGNHVLCAYIYKPANGYGNVEVAAHFAAESSTGTNVEVCTTDDFTKGVDALVYEVSDASNGDS......LMKIAYPVELFDRNIIDGRAMLASFLTLCIGNNQGMGDVAYAKMHDFYVPRQYLELFDGPSKNIADFWRMLGRPTENGGMIAGTIVKPKLGLRPKPFADACYHFWLGGDFVKNDEPQGNQVFAPLKETITAVADAMRRAQDETGEAKIFSANITADDPREMIARGEFILNAFGE..NASRVAFLVDGYVAGPTAITTARRNFPNQFLHYHRAGHGAVTSPQAKRGYTAFVLSKMSRLQGASGIHTGTMGFGKMEGEMADKSMAYMIEREEAQGPYFKQKWYGMKATTPMISGGMNALRLPGFFDNLGHSNICQTSGGGAFGHLDGPTAGALSLRQSHDAWIQGVNLLDYAKEHNELARAFESFPGDADRFYPTWRHQL.... [uniref90|E6VVI6 Ribulose-bisphosphate carboxylase n=1 Tax=Desulfovibrio aespoeensis Aspo-2 RepID=E6VVI6_DESAO]
Q8RTI1  : MDQSNRYADLSLKEDDLIKGGNHVLVAYLMKPKTGYGYLEAAAHFSAESSTGTNVEVSTTDDFTKGVDALVYEIDEAK.........EIMKIAYPVDLFDRNITDGRAMIVSFLTLAIGNNQGMGDIAYAKMLDFYVPQKYLRLFDGPSKDISDLWRILGRPVVNGGYIAGTIIKPKLGLRPKPFAEAAYQFWLGGDFIKNDEPQGNQVFSPMRETIPLVYDSMKRAMDETGEAKLFSANITADDHYEMMARGEFILNTFGP..DADKVAFLVDGYVGGPGMVTTARRHFANQYLHYHRAGHGAVTSPSAKRGYTAFVLAKMSRLQGASGIHVGTMGYGKMEGDATDKNIAYMIERDSADGPFYHQEWYGMKPTTPIISGGMNALRLPGFFENLGHANLINTSGGGSYGHIDSPAAGAISLRQAYECWQQGADPIEFAKEHKEFARAFESFPGDADTIFPGWREKLGVHK [uniref90|Q8RTI1 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II n=1 Tax=magnetite-containing magnetic vibrio RepID=Q8RTI1_9PROT]
Q0F2Z8  : MDQSNRYADLSLNEADLIAGGKHLLVAYKLIPAKGYGFLEVAAHIAAESSTGTNVEVSTTDDFTRGVDALVYDIDETAFGDEGVTGGGLMKVAYPVELFDPNLIDGHYNVSHMWSLILGNNQGMGDHEGLRMLDFMVPECMIRKFDGPSAGIADLWKVLGRPEVDGGYISGTIIKPKLGLRPEPFAKACLDFWLGGDFIKNDEPQANQPFCPMKVVIPKVAEAMDRAQQETGQAKLFSANATADYHGECVARGEYILSEFAKYGNEKHVAFLIDGFVTGPAGVTTARRAFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLARLQGASGIHTGTMGYGKMEGHGKETVLAYMLERDECMGHYFNQKWYGMKPTAPIISGGMNALRLPGFFENLGHGNVINTCGGGSFGHIDSPAAGGKSLDQAYDCWKSGTDPIEYAKTHGEFARAFESFPGDADKLYPGWRDKLGVHK [uniref90|Q0F2Z8 Ribulose-bisphosphate carboxylase n=1 Tax=Mariprofundus ferrooxydans PV-1 RepID=Q0F2Z8_9PROT]
SecStr  : CCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCEEECCCCCCHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCEEEECCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEECCCCCCHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCHHCCCCCCCEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHHHHCCCC [Secondary structure predicted by PsiPred]
Target  : MDQSNRYANLNLKEEDLIKNGKHLLVAYKLIPAKGHGFLEVAAHVAAESSTGTNVEVSTTDDFTRGVDALVYEIDETAFGDDPVKGGGLFKVAYPVELFDPNLTDGTYNISHMWSLILGNNQGMGDHQGLRMLDFLVPEMMVRKFDGPSANISNLWKVLGRSETDGGYIAGTIIKPKLGLRPEPFAKACYDFWLGGDFIKNDEPQANQPFCPMEVVMPKVAEAMDRAQQATGQAKLFSANITADYYKEMIHRGDFVLETFAKYNSASHVAFLVDGFVTGPAGVTTARREFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLVRLMGASGMHTGTMGYGKMEGHGKETVLAYMLERDECQGPYFYQKWYGMKATTPIISGGMNALRLPGFFQNLGHGNVINTCGGGAFGHIDSPAAGGISLGQAYDCWKSGSDPIEYAKTHKEFARAFESFPKDGDKLFAGWREKLGVHK
Match   : MDQSNRYANLNLKE:|LI :G|H:L AY | P    :F||:AAH AAESSTGTNVEV TTDDFTRGVDALVYE|DE:          :L:K|AYP|ELFD N: DG   I: : :L |GNNQGMGD |  |M DF VP   :| FDGPS::I::LW|VLGR   :GG|I:GTIIKPKLGLRP|PFA:ACYDFWLGGDFI:NDEPQ:NQ F:P:: ::  VA|AM RAQ: TG|AKLFS NITAD | EM| RG|F|LETFA     :H|AFLVD   ::PA:VTTARR FP  |LH|HRAGHGAVTS :S  G   :   K|:RL:GASG:HTGTMG|GKMEG:: | :|AYM| :D ::GPYF|Q:W GM: TTPIISGGMNALR|PGFF:NLGH:N:I T:GGGAFGH|D: AAG: SL QA :CWK:G:DP|E|AK H|EFARAFESFP:D:DKL| :WR KL    
Template: MDQSNRYANLNLKESELIAGGRHVLCAYIMKPK...NFIQTAAHFAAESSTGTNVEVFTTDDFTRGVDALVYEVDEA..........SLMKIAYPIELFDRNVIDGRAMIASFLTLTIGNNQGMGDVEYAKMYDFYVPPAYLKLFDGPSTTIKDLWRVLGRPVINGGFIVGTIIKPKLGLRPQPFANACYDFWLGGDFIXNDEPQGNQVFAPFKDTVRAVADAMRRAQDKTGEAKLFSFNITADDHYEMLARGEFILETFAD....DHIAFLVD.GYVAPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHTGTMGFGKMEGEAADRAIAYMITEDAADGPYFHQEWLGMNPTTPIISGGMNALRMPGFFDNLGHSNLIMTAGGGAFGHVDGGAAGAKSLRQAEQCWKQGADPVEFAKDHREFARAFESFPQDADKLYPNWRAKL....
SecStr  : CCHHHHHCTTTTHHHHHHHHCCCEEEEEEEECC...HHHHHHHHHHHHHCCCCCCCTTTTHHHHHHCCCEEEEEETT..........EEEEEEETTTTCCCCCCCCCCCHHHHHHHHHGGGGCTTTTEEEEEEEEECHHHHHHCCCCCCCCHHHHHHHHHCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCEEEEETTTTCCTTTTHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCHHHHHHHHHHHHHHHHHC....TEEEEEEH.HHHHHHHHHHHHHHHCCCEEEEETTTTCCCCTTTTCCCCHHHHHHHHHHHHHCEEEEECTTTTCCCCCTTTTHHHHHHHHCEEEECCCEEEEETTTCCCEEEECCCCCCCHHHHHHHHHHCCCEEEEEHHHHHHCCCHHHHHHHHHHHHHHHHHHCCHHHHHHHCHHHHHHHHHHCHHHHHHHHCCTTTTC.... [Secondary structure assigned by YASARA]
1RSC-G  : ....LTYYTPDYTP.....KDTDLLAAFRFSPQ.....DEAGAAIAAESST..........TDMDRYKGKCYHIEP............FAFIAYPLDLFEE.......SVTNILTSIVGNVFGFKAIRSLRLEDIRFPVALVKTFQGPPHGIQVERDLLNKY....RPMLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKSQAETGEIKGHYLNVTAPTCEEMMKRAEFAKEL..........IIMHD.FLTAFTANTTLAKWCRGVLLHIHRAMHAVIDR...NHGIHFRVLAKCLRLSGGDHLH..............TLGFVDLMREDHIEA.FFTQDWASMPGVLPVASGGIHVWHMPALVEIF.GDDSVLQFGGGTLGHPWGNAPGATANRVALEACVQ...LREAGKWSPELAAALDLW................... [: RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (LARGE]
1GEH-B  : ..........GYEP.......RDIIAVFRVTPA.....EQAAGAVAAESST.GTWT..YEQERWADLSAKAYDFHD............IVRIAYPFHAFEE.......NLPGLLASIAGNIFGMKRVKGLRLEDLYFPEKLIREFDGPAFGIEGVRKMLEIK....RPIYGVVPKPKVGYSPEEFEKLAYDLLSNADYMKDDENLTSPWYNRFEERAEIMAKIIDKVENETGEKKTWFANITAD.LLEMEQRLEVLADL..........HAMVD.VVITWGALRYIRDLAAGLAIHGHRAMHAAFTR...YHGISMFVLAKLYRLIGIDQLH..............VIQNARILRESHYK...LEQKFYSIKAAFPTSSGGLHPGNIQPVIEAL.GTDIVLQLGGGTLGHPDGPAAGARAVRQAIDAIMQGIPLDEYAKTHKELARALEKW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE]
1SVD-A  : .....TYWMPEYTP.....LDSDILACFKITPQ.....EEAAAAVAAESSTG..........DMDYYKGRAYRIED............YAFIAYPIDLFEE.......SVVNVFTSLVGNVFGFKAVRGLRLEDVRFPLAYVKTCGGPPHGIQVERDKMNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFMRWRDRFLFVQDATETAEAQTGERKGHYLNVTAPTPEEMYKRAEFAKEI..........IIMHD.YITGFTANTGLAKWCQGVLLHIHRAMHAVIDR...NHGIHFRVLTKILRLSGGDHLH..............TLGWIDLLRESFIP..FFDQDWGSMPGVFAVASGGIHVWHMPALVNIF.GDDSVLQFGGGTLGHPWGNAAGAAANRVALEACVE...LTAAAQHSPELKIAMETW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE]
2YBV-A  : ......YYTPDYTP.....KDTDILAAFRVTPQ.....EEAAAAVAAESSTG........LTDLDRYKGCCYDIEP............IAYIAYPLDLFEE.......SVTNMLTSIVGNVFGFKALKALRLEDLRIPVAYLKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKAQAETGEIKGHYLNVTAPTCEEMLKRAEFAKEL..........IIMHD.FLTAFTANTTLSKWCRGMLLHIHRAMHAVMDR...NHGIHFRVLAKCLRMSGGDHIH..............TLGFVDLLRENYIE..YFTQDWASMPGVMAVASGGIHVWHMPALVDIF.GDDAVLQFG.....HPWGNAPGATANRVALEACIQ...IREAARWSPELAAAC...................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN]
1BXN-C  : ....MGYWDGDYVP.....KDTDLLALFRITPQ.....VEAAAAVAGESST..WTV......ACDMYRAKAYRVDP............FCYVAYDLSLFEE.......SIANLTASIIGNVFSFKPIKAARLEDMRFPVAYVKTFAGPSTGIIVERERLDKF....RPLLGATTKPKLGLSGRNYGRVVYEGLKGLDFMKDDENINSQPFMHWRDRFLFVMDAVNKASAATGEVKGSYLNVTAGTMEEMYRRAEFAKSL..........IIMVD..LIVWTCIQSMSNWCRDMILHLHRAGHGTYTR...NHGVSFRVIAKWLRLAGVDHMH..............VQGYYNVCRDAYTQ..FFDQDWASLRKVMPVASGGIHAGQMHQLIHLF.GDDVVLQFGGGTIGHPQGIQAGATANRVALEAMVL...LRDAARWCGPLRAALDTW................... [: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)]
1EJ7-L  : .....TYYTPEYQT.....KDTDILAAFRVTPQ.....EEAGAAVAAESSTGTWTTV.....SLDRYKGRCYRIER............IAYVAYPLDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENVNSQPFMRWRDRFLFCAEALYKAQAETGEIKGHYLNATAGTCEEMIKRAVFAREL..........IVMHD.YLTGFTANTSLAHYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHIH..............TLGFVDLLRDDFVE..YFTQDWVSLPGVLPVASGGIHVWHMPALTEIF.GDDSVLQFGGGTLGHPWGNAPGAVANRVALEACVK...IREACKWSPELAAACEVW................... [: RUBISCO (LARGE SUBUNIT)]
1IWA-C  : ....MGYWNPDYQV.....KDTDVLALFRVTPQ.....IEAAAAVAGESST...........AADLYRAKAYKVDQ............FAYIAYELDLFEE.......SIANLTASIIGNVFGFKAVKALRLEDMRLPLAYLKTFQGPATGVILERERLDKF....RPLLGCTTKPKLGLSGKNYGRVVYEALKGLDFVKDDENINSQPFMRWRERYLFTMEAVNKASAATGEVKGHYLNVTAATMEEMYARANFAKEL..........IIMID..LVIYTAIQTMAKWARDMILHLHRAGNSTYSR...NHGMNFRVICKWMRMAGVDHIH..............TRGFYKTLLLPKLE..FFDMEWASLRKVMPVASGGIHAGQMHQLIHYLG.EDVVLQFGGGTIGHPDGIQAGATANRVALEAMIL...LREAAKTCGALRTALDLW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE]
1TEL-B  : .....GFFAS...........QYLVLDYYLESV.....ETALAHFCSEQSTA........DEDFRVHAAKVIDYEV............RVTIAHPHCNFGP.......KIPNLLTAVCGETYFTPGVPVVKLMDIHFPDTYLADFEGPKFGIEGLRDILNAH....RPIFFGVVKPNIGLSPGEFAEIAYQSWLGLDIAKDDEMLADVTWSSIEERAAHLGKARRKAEAETGEPKIYLANITDE.VDSLMEKHDVAVRN..........ALLIN.ALPVLSAVRMLSNYT.QVPLIGHFPFIASFSR...KYGIHSKVMTKLQRLAGLDAVI..............VLENVIECTKP..........MGRIKPCLPVPGGSDSALTLQTVYEKVGNVDFGFVPGRGVFGHPMGPKAGAKSIRQAWEAIEQGISIETWAETHPELQAMVDQ.................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE, LARGE SUBUNIT]
2D69-A  : .....DFVDLNYEP.....GRDELIVEYYFEPN.....EEAAGRIASESSIGTW.........AKRSMAKVFYLEK............IAKIAYPLTLFEE.......SLVQLFSAVAGNVFGMKALKNLRLLDFHPPYEYLRHFKGPQFGVQGIREFMGVK....RPLTATVPKPKMGWSVEEYAEIAYELWSGIDLLKDDENFTSFPFNRFEERVRKLYRVRDRVEAETGETKEYLINITGP.VNIMEKRAEMVANE..........YVMID.IVVAWSALQYMREVTEGLAIHAHRAMHAAFTR...RHGITMLALAKAARMIGVDQIH..............IKRINDFLLS...........WEHIRPVFPVASGGLHPGLMPELIRLF.GKDLVIQAGGGVMGHPDGPRAGAKALRDAIDAAIEGVDLDEKAKSSPELKKSLREV................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE]
2QYG-D  : .....GFYAK...........NYIELDFDFECA.....HEAAAHLCSEQSTA...........RPRFAAKVLELSA............RVTIAHPHGNF........AKIPNLLSAVCGEVFFSPGIPLIRLQDIRFPEPYLAAFDGPRFGIAGVRERLQAF....RPIFFGVIKPNIGLPPQPFAELGYQSWTGLDIAKDDEMLADVDWCPLAERAALLGDACRRASAETGVPKIYLANITDE.VDRLTELHDVAVAN..........ALLIN.AMPVLSAVRMLRKHA.TVPLIAHFPFIAAFSR...NYGIHSRVMTRLQRLAGFDVVI..............VLDCIRACLE...........MGPIKPCLPVPGGSDSAATLENVYRKVGSADFGFVPGRGVFGHPMGPAAGATSIRQAWDAIAAGIPVPDHAASHPELAAALRAF................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE-LIKE PROTEIN 2]
2V67-A  : ....LTYYTPDYVV......DTDILAAFRMTPQ.....EECGAAVAAESST...........SLDRYKGRCYDIEP............IAYVAYXIDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFVGXPHGIQVERDKLNKY....RGLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTXDDENVNSQPFMRWRDRFLFVAEAIYKAQAETGEVKGHYLNATAGTCEEMMKRAVXAKEL..........IIMHD.YLTGFTANTSLAIYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHLH..............ILGFVDLMRDDYVE..YFTQDWXSMPGVMPVASGGIHVWHMPALVEIF.GDDACLQFGGGTLGHPWGNAPGAAANRVALEACTQ...IRSACKWSPELAAACEVW................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN]
3NWR-A  : ....................EDTLEADYLIET......ARVADVMAGEQSSG............ARSRASVLRIEE............RITLSFPLANI.........NLPTLAATVAGNLYDLGEVTGVRLLSLRLPASYRARFELPRHGVAGTRALTDVK....RPMIGTIIKPNVGLSAAETAALVRELCEAVDFIXDDEVCANPAHAPLAERVRAVMSEVRRYRERSGRPVMVAFNITDD.LDAMRRHAELVERE..........CVMAS.INWCFSAIQSLRRTT.PLVLHAHRNGYGMMSR...ALGMSFQAYQTLWRLSGVDHMH..............VIESARDCATP...............AVLPAFSSGQWAGTVQATFDAVRSTDLLFMSGGGILAHPDGPAAGVTSVRQAWAAVQAGTPLPVYAEHMPELRRALAFF................... [: A RUBISCO-LIKE PROTEIN]
3QFW-B  : ......................RIVATYHIAS......EQRALALAIEQSVEC............NIVGRVEDVAE............AVRIGLAAATAP.......AEPGQLLNMLFGNSSIQPD...IALADVELPAHYLTAFGGPRVGLAGIRTLTGAQ....RALTASALKP.QGLSPAALASIAHQLALGVDLIKDDHGLADQAFSPFAERAAAVGKAVREANAARGGRTLYAPNISG.TLDDMRRQLGVIRDE..........AVLVA.PMIVVSNFHAIVKEAAGLVVVAHPAMAGAA........IAAPLLGRLFRLFGADATV..............CLALAQAARD...........FGKLNACIPTPAGGIMLQRVNELLRFYG.QDVMLLI..........LTEQASRFVNKVADYGQR....................................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE]
uniref90: ......................RIIVTYQVAA......AARAEALAIEQSVEC............EIVGRVEAIAP............SVRVSLASATAP.......AEPGQLLNMLFGNSSIQPD...VTLADVELPPAYPAAFGGPKLGISGLRAKLGAP....RALTGSALKP.QGLAPEALAGLAHRLALGVDLIKDDHGIADQAFSPFAARVPAVARAMREACAVRGAAMLYAPHVSG.SLDDMRRQLDIVRRE..........VVMLM.PMIVLANFHLIAKEAEGLIVLAHPSLAGAQ........IAPDLLGKLFRLLGADATI..............CRALADAARR...........WHDLKPCLPVPAGGIAIDRIKELLAFYG.TDVMLLI..........LTEHAARFTAEVASHGQ........................................ [uniref90|Q6N7T7 Ribulose bisphosphate carboxylase-like protein 1 n=2 Tax=Rhodopseudomonas palustris RepID=RBLL1_RHOPA]
2ZVI-A  : ......................ELLATYLLT.......EKKAEQIATGLTVG...........MQKHKGRVIKVEE............VITIAYPEINFSQ.......DIPALLTTVFGKLSL...DGKIKLIDLHFSEAFKRALPGPKFGVYGIRKLLGE.....RPLLMSIFKGVIGRDLSDIKEQLRQQALGVDLIKDDEIFFETGLAPFETRIAEGKQILKETYEQTGHKTLYAVNLTGR.TADLKDKARRAAEL..........ALLFN.VFAYLDVMQGLAED..PVPIMAHPAVSGAFTS...FYGFSHALLGKLNRYCGADFSL..............ALAIHEECVR.............AFNQTFAVPSAGIHPGMVPLLMRDF.GIDHIINAGGGVHGHPNGAQGGGRAFRAIIDAVLEAQPIDEKAEQCKDLKLALDKWGK................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE]
uniref90: ......................................HKQAKIIAVGQTAG...........LRQHLAEVIEIKT..............KIRFPEINVEN.......DLASLLTMIFGKYSM...AGAAKVIGVHLPESYGQR...PKFGITGIRKILNV.....RPLIMAIFKPALGLSAADHAVILKQVADALDIIKDDEILGDLETAPTLKRLEACRQVLEAIKQQTGRTVLYAVNVTGK.ADKLIEKARLLVKE..........ALLLN.VLTYFSVLEALAAD..NVPIFAHPAFAGAMCA...DTGLSYSVIGRFMAHGGVDAVL..............EKKIRDSLRS.............VF....PVPSAGIHPGIVPKAIADY.GDDVILNAGTGIMDHPNNPGAGVKAFFEALERVKTGQSFTLDTVPEGALKQALQKWG.................. [uniref90|B7KIK8 Ribulose-bisphosphate carboxylase n=1 Tax=Cyanothece sp. PCC 7424 RepID=B7KIK8_CYAP7]
2OEK-B  : ......................AVMATYLLHDE.....RKKAEGIALGLTIG...........LRKHKGEVVAIEE............IVKIAYPTVNFSA.......DLPALLVTTFGKLSLD...GEVRLLDLEFPDEWKRQFPGPRFGIDGIRDRVGVH....RPLLMSIFKGMIGRDLAYLTSELKKQALGVDLVXDDEILFDSELLPFEKRITEGKAALQEVYEQTGKRTLYAVNLTGK.TFALKDKAKRAAEL..........VLLFN.VFAYLDVLQALRED..AVPIMAHPAFSGAVTP...FYGVAPSLWGKLLRLAGADFVL..............ALGIARALTD.............PFARAFPVPSAGIHPGLVPLIIRDF.GLDTIVNAGGGIHGHPDGAIGGGRAFRAAIDAVLAGRPLRAAAAENEALQKAIDRWGV................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE ENOLASE]
uniref90: .......................VIATYRLAGG.....TKKAETIALGMTVG...........LQRHAGRVVSVDA............LIRIAYPLANLTP.......DLPSLLTATFGKLSMD...GKIRLLDLTLPPTFAAAFPGPKLGVEGIRERLGVH....RPLLMSIFKSCVGLTLAELAEGFFQQALGVDLIKDDEIFFNDTDAPFEQRLEACLQATERARRETGQTVLYAINLTGP.VHRLPEKARRAARL..........ALLIN.VLPYFDLLQRLAED..TVPLIAHPALAGALYP...DYGIAAPLLGTLMRLAGADLVL..............ALGLASRLTD.............PHRPTFPVPSAGIHPGLVPHMMDDF.GLDVVINAGGGIHGHPGGAAAGGRAFRAAIAAGVGGVPLEQAAAGSRDLRAALDQWG.................. [uniref90|D5MLU6 2,3-diketo-5-methylthiopentyl-1-phosphate enolase (DK-MTP-1-P enolase) n=1 Tax=NC10 bacterium 'Dutch sediment' RepID=D5MLU6_9BACT]
3FK4-A  : ......................GIIATYLIHDD.....EKKAEQIALGLTIG...........LKQHKGNVIHVEE............IIKIEYPLLNFSP.......DLPAILTTTFGKLSLD...GEVKLIDLTFSDELKKHFPGPKFGIDGIRNLLQVH....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENALTPLTKRIVSGKEVLQSVYETYGHKTLYAVNLTGR.TFDLKENAKRAVQA..........ILLFN.VFAYLDVLQSLAED..PVPIMAHPAVSGAYSA...LYGVSSPLLGKLLRYAGADFSL..............ALAISKYLTE...........DASFKKSFSVPSAGIHPGFVPFIVRDF.GKDVVINAGGGIHGHPNGAQGGGKAFRTAIDATLQNKPLHEV..DDINLHSALQIWG.................. [: RUBISCO-LIKE PROTEIN]
uniref90: ......................GIIATYLIHDD.....EKKAEQIALGLTIG...........LKQHKGNVLHVEE............IIKIEYPLLNFSP.......DLPAILTTTFGKLSLD...GEVKLIDLTFSDELKKHFPGPKFGIDGIRNLLQVH....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENALTPLTNRIVSGKEVLQSVYETYGHKTLYAVNVTGR.TFDLKENAKRAVQA..........ILLFN.VFAYLDVLQSLAED..PVPIMAHPAVSGAYSA...LYGISSPLLGKLLRYAGADFSL..............ALAISKYLTE...........DVFFKKSFSVPSAGIHPGFVPFIIRDF.GKDVVINAGGGIHGHPNGAQGGGKAFRTAIDATLQNKPLHEV..DDINLHSALQIWG.................. [uniref90|C3P745 2,3-diketo-5-methylthiopentyl-1-phosphate enolase n=71 Tax=Bacillus cereus group RepID=MTNW_BACAA]

NOTE: To save space, only 20 of 1110 template profile alignments are shown above. The complete set of alignments can be found in the file Homology_5han-~_profile.ali. The template profile contains structural alignments of 16 PDB files, which provide safe anchors for the remaining sequence-based alignments (only reliable regions shown).

In the alignment above, 448 of 470 target residues (95.3%) are aligned to template residues. Among these aligned residues, the sequence identity is 64.5% and the sequence similarity is 75.9% ('similar' means that the BLOSUM62 score is > 0). The following 6 loops had to be modeled (only the first of 2 similar loops in the homodimer is listed):

LoopN-terminal anchorLoop sequenceC-terminal anchor
1VDGFVTGPAGVT
3VAFLVDGFVTGP
5KLIPAKGHGFLEV
7ETFAKYNSASHVAF
9EIDETAFGDDPVKGGGLFKV
11WREKLGVHKNone

After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).

The resulting half-refined model has been saved as Homology_5han-~03_refined050.yob and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals-0.049Good
Packing 1D-0.745Good
Packing 3D-1.332Satisfactory
Overall-0.917Good

Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as Homology_5han-~03_refined100.yob, the corresponding Z-scores are listed below:

Check typeQuality Z-scoreComment
Dihedrals0.263Optimal
Packing 1D-0.537Good
Packing 3D-1.378Satisfactory
Overall-0.812Good

Since the overall quality Z-score improved to -0.812 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.

NOTE: 8 residues contained in N- and C-terminal unaligned tails of the homodimeric model have been excluded from the Z-scores in both tables above, since they are not reliable (YASARA does not yet perform ab initio structure prediction) and would have mainly added noise to the result.

The final model for this template and alignment has been saved as Homology_5han-~03.yob, and is shown below, together with a plot of its overall quality Z-score, shown per residue:

6.11. Homology model 11/15, based on template 5HAN-~, alignment variant 04

This model is a homodimer, and based on the following profile-profile alignment:

(To improve readability, only up to ten lines of the complete target multiple sequence alignment (MSA) shown above are also displayed here (upside down). The template MSA has been shrunk and focused on structurally aligned PDB entries. The actual target-template alignment can be found in the middle at the line named 'Match'.)

Q08EW6  : .......................................................................................................................NNQGGGDIEHAKIHGIYMPERAIQLFDGPSKDISDMWRILGRPVKDGGYNAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEIQGNQVFSPMNQTIPLVVDAMKRAQDETGQAKLFSANITADDQYEMCARADFILEAFGP..DADKVAFLVDGYVGDPGMITTARSQYPNQYLHYHRAGHGAVNSPKIKRGYTAFVLAKMSRLQGASGAHVGTMGYGKME................................................................................................................................ [uniref90|Q08EW6 Ribulose 1,5-bisphosphate carboxylase/oxygenase large subunit (Fragment) n=1 Tax=uncultured marine bacterium RepID=Q08EW6_9BACT]
Q5DVV5  : ............................................................................................................................................................................IIKPKLGLRPKPFAEACYNFWLGGDFIKNDEPQGNQIWGPIKEVVPLVKDSLVRAQDDTGMAKLFSFNITADDHYEMLHRGEYILETFAEFSE..NIAFLVDGCVGGPGMVTTARRNFPDQFLHYHRAGHGAVTSDQSDRGYNMLVHMKMARLQGASGIHTGTMGYGKMEGAADDKVIAYMLERDSADGLSYHQEWEGMKATTPIICGGMNA...................................................................................... [uniref90|Q5DVV5 Ribulose-1,5-bisphosphate carboxylase oxygenase large subunit (Fragment) n=11 Tax=uncultured prokaryote RepID=Q5DVV5_9ZZZZ]
Q933G7  : ........................................................................................................................................VPPAYLRLFDGPSTTIKDLWRVLGRPVVDGGFIVGTIIKPKLGLRPQPFADACYDFWLGGDFIKNDEPQGNQVFAPFKDTVRAVNDAMRRAQDATGQPKLFSFNITADDHYEMLARGEYILETFGE..NADHVAFLVDGYVAGPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHVGTMGYGKMEGEASDRDSAFMITQDSAEGPYFKQEW...................................................................................................... [uniref90|Q933G7 Form II ribulose 1,5-bisphosphate carboxylase/oxygenase (Fragment) n=5 Tax=Rhodopseudomonas palustris RepID=Q933G7_RHOPA]
F2ZCE9  : .....................................................................................................................................DFYVPPDFLRLFDGPATTISNLWRVLGRPHQNGGFIVGTIVKPKLGLRPRPFADACYDFWLGGDFIKNDEPQGNQTFSPLKETIPLVADAMRRAQDETGEAKLFSANITADDHYEMVARGEFILDTFGEF..ADHVAFLVDGYVAGAAAVTTARRSFPQQYLHYHRAGHGAITSPQSKRGYTAFVHCKMARLQGASGIHTGTMSFGKMEGEAADRAIAFMLEQDSADGPYFHQEWHGMNPTTSIISG.......................................................................................... [uniref90|F2ZCE9 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=1 Tax=uncultured bacterium RepID=F2ZCE9_9BACT]
F2ZCD0  : ......................................................................................................................GNNQGMGDIANAQMQDFYVPPAMLALFDGPAKSINDLWTLLGRDNENGGYIAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEPQGNQVFCPLKKVLPLVHDAMKRAQDETGEAKLFSLNITADDHYEMCARADFGLETFGE..DAPRLAFLVDGFVGGPGMVTTARRQYSSQYLHYHRAGHGMITSPSSKRGYTAYILAKMSRLMGASGIHVGTMGYGKMEGGADDKIIAYMIERDECQGPFYYQKWHGMKPTTPIVSGGM........................................................................................ [uniref90|F2ZCD0 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=4 Tax=uncultured bacterium RepID=F2ZCD0_9BACT]
F5BZE6  : ......................................................................................................................GNNQGMGDVEYAKMIDFYMARSLLTLFDGPAMNITDMWRVLGRPQVNGGMVVGTIIKPKLGLRPKPFADACYMFWMGGDFIKNDEPQGNQVFAPTREIIPLVAEAMERAQQETGEAKIFSANITADDPFEMIRRGEFILEAFGK..NASHVAFLVDGYVGGPSAVTLCRRYFPNQFLHYHRAGHGAVTSNQSKRGYTVLTHMKMSRLQGASGIHTGTMGYGKMEGDKNEKMVAYMIERDEAMGVYYNQPWHGMTATTPIISGGMNALR.................................................................................... [uniref90|F5BZE6 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II (Fragment) n=1 Tax=alpha proteobacterium LM-5 RepID=F5BZE6_9PROT]
Q9FPW1  : LDQSSRYADLSLDEATLVKNGKHVLVAYIMKPKAGYDYLATAAHFAAESSTGTNVNVCTTDDFTKSVDALVYYIDPDSEE.........MKIAYPTLLFDRNIIDGRGMMCSFLTLAIGNNQGMGDVEYGKIYDFYLPPSFLRLYDGPAVNVEDMWRILGKGTSNGGLVDGTIIKPKLGLQPNPFGEACYSFWQGGDFIKNDEPQGNQVFCQMNECIPEVVKAMRACVKETGSSKLFSANITADDPEEMIARGKYIMSQFGPLSE..NCAFLVDGYVAGGTAVTCCRRNFPKQFLHYHRAGHGSVTSPQTQRGYTAFVHTKISRVIGASGIHVGTMSFGKMEGDASDKNIAYMLQDDEADGPYYRQEWQGMKETTPIISGGMNALRLPAFFENLGHSNVILTAGGGSFGHKDGPKIGAISCRQGEEAWKSLSDVIEYAKTHEEIKGAFLTFQKDADQIYPGWKEKLG... [uniref90|Q9FPW1 Ribulose 1,5-bisphosphate carboxylase oxygenase large subunit n=1 Tax=Symbiodinium sp. RepID=Q9FPW1_SYMSP]
E6VVI6  : .DQTSRYVNFDLKEDQLIADGNHVLCAYIYKPANGYGNVEVAAHFAAESSTGTNVEVCTTDDFTKGVDALVYEVSDASNGDS......LMKIAYPVELFDRNIIDGRAMLASFLTLCIGNNQGMGDVAYAKMHDFYVPRQYLELFDGPSKNIADFWRMLGRPTENGGMIAGTIVKPKLGLRPKPFADACYHFWLGGDFVKNDEPQGNQVFAPLKETITAVADAMRRAQDETGEAKIFSANITADDPREMIARGEFILNAFGE..NASRVAFLVDGYVAGPTAITTARRNFPNQFLHYHRAGHGAVTSPQAKRGYTAFVLSKMSRLQGASGIHTGTMGFGKMEGEMADKSMAYMIEREEAQGPYFKQKWYGMKATTPMISGGMNALRLPGFFDNLGHSNICQTSGGGAFGHLDGPTAGALSLRQSHDAWIQGVNLLDYAKEHNELARAFESFPGDADRFYPTWRHQL.... [uniref90|E6VVI6 Ribulose-bisphosphate carboxylase n=1 Tax=Desulfovibrio aespoeensis Aspo-2 RepID=E6VVI6_DESAO]
Q8RTI1  : MDQSNRYADLSLKEDDLIKGGNHVLVAYLMKPKTGYGYLEAAAHFSAESSTGTNVEVSTTDDFTKGVDALVYEIDEAK.........EIMKIAYPVDLFDRNITDGRAMIVSFLTLAIGNNQGMGDIAYAKMLDFYVPQKYLRLFDGPSKDISDLWRILGRPVVNGGYIAGTIIKPKLGLRPKPFAEAAYQFWLGGDFIKNDEPQGNQVFSPMRETIPLVYDSMKRAMDETGEAKLFSANITADDHYEMMARGEFILNTFGP..DADKVAFLVDGYVGGPGMVTTARRHFANQYLHYHRAGHGAVTSPSAKRGYTAFVLAKMSRLQGASGIHVGTMGYGKMEGDATDKNIAYMIERDSADGPFYHQEWYGMKPTTPIISGGMNALRLPGFFENLGHANLINTSGGGSYGHIDSPAAGAISLRQAYECWQQGADPIEFAKEHKEFARAFESFPGDADTIFPGWREKLGVHK [uniref90|Q8RTI1 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II n=1 Tax=magnetite-containing magnetic vibrio RepID=Q8RTI1_9PROT]
Q0F2Z8  : MDQSNRYADLSLNEADLIAGGKHLLVAYKLIPAKGYGFLEVAAHIAAESSTGTNVEVSTTDDFTRGVDALVYDIDETAFGDEGVTGGGLMKVAYPVELFDPNLIDGHYNVSHMWSLILGNNQGMGDHEGLRMLDFMVPECMIRKFDGPSAGIADLWKVLGRPEVDGGYISGTIIKPKLGLRPEPFAKACLDFWLGGDFIKNDEPQANQPFCPMKVVIPKVAEAMDRAQQETGQAKLFSANATADYHGECVARGEYILSEFAKYGNEKHVAFLIDGFVTGPAGVTTARRAFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLARLQGASGIHTGTMGYGKMEGHGKETVLAYMLERDECMGHYFNQKWYGMKPTAPIISGGMNALRLPGFFENLGHGNVINTCGGGSFGHIDSPAAGGKSLDQAYDCWKSGTDPIEYAKTHGEFARAFESFPGDADKLYPGWRDKLGVHK [uniref90|Q0F2Z8 Ribulose-bisphosphate carboxylase n=1 Tax=Mariprofundus ferrooxydans PV-1 RepID=Q0F2Z8_9PROT]
SecStr  : CCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCEEECCCCCCHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCEEEECCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEECCCCCCHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCHHCCCCCCCEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHHHHCCCC [Secondary structure predicted by PsiPred]
Target  : MDQSNRYANLNLKEEDLIKNGKHLLVAYKLIPAKGHGFLEVAAHVAAESSTGTNVEVSTTDDFTRGVDALVYEIDETAFGDDPVKGGGLFKVAYPVELFDPNLTDGTYNISHMWSLILGNNQGMGDHQGLRMLDFLVPEMMVRKFDGPSANISNLWKVLGRSETDGGYIAGTIIKPKLGLRPEPFAKACYDFWLGGDFIKNDEPQANQPFCPMEVVMPKVAEAMDRAQQATGQAKLFSANITADYYKEMIHRGDFVLETFAKYNSASHVAFLVDGFVTGPAGVTTARREFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLVRLMGASGMHTGTMGYGKMEGHGKETVLAYMLERDECQGPYFYQKWYGMKATTPIISGGMNALRLPGFFQNLGHGNVINTCGGGAFGHIDSPAAGGISLGQAYDCWKSGSDPIEYAKTHKEFARAFESFPKDGDKLFAGWREKLGVHK
Match   : MDQS :    NLKE:|LI :G|H:L AY | P    :F||:AAH AAESSTGTNVEV TTDDFTRGVDALVYE|DE:          :L:K|AYP|ELFD N: DG   I: : :L |GNNQGMGD |  |M DF VP   :| FDGPS::I::LW|VLGR   :GG|I:GTIIKPKLGLRP|PFA:ACYDFWLGGDFI:NDEPQ:NQ F:P:: ::  VA|AM RAQ: TG|AKLFS NITAD | EM| RG|F|LETFA   :A:H|AFLVDG|V:GPA:VTTARR FP  |LH|HRAGHGAVTS :S  G   :   K|:RL:GASG:HTGTMG|GKMEG:: | :|AYM| :D ::GPYF|Q:W GM: TTPIISGGMNALR|PGFF:NLGH:N:I T:GGGAFGH|D: AAG: SL QA :CWK:G:DP|E|AK H|EFARAFESFP:D:DKL| :WR KL    
Template: MDQS.NRY..NLKESELIAGGRHVLCAYIMKPK...NFIQTAAHFAAESSTGTNVEVFTTDDFTRGVDALVYEVDEA..........SLMKIAYPIELFDRNVIDGRAMIASFLTLTIGNNQGMGDVEYAKMYDFYVPPAYLKLFDGPSTTIKDLWRVLGRPVINGGFIVGTIIKPKLGLRPQPFANACYDFWLGGDFIXNDEPQGNQVFAPFKDTVRAVADAMRRAQDKTGEAKLFSFNITADDHYEMLARGEFILETFAD..NADHIAFLVDGYVAGPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHTGTMGFGKMEGEAADRAIAYMITEDAADGPYFHQEWLGMNPTTPIISGGMNALRMPGFFDNLGHSNLIMTAGGGAFGHVDGGAAGAKSLRQAEQCWKQGADPVEFAKDHREFARAFESFPQDADKLYPNWRAKL....
SecStr  : CCHH.HHH..TTHHHHHHHHCCCEEEEEEEECC...HHHHHHHHHHHHHCCCCCCCTTTTHHHHHHCCCEEEEEETT..........EEEEEEETTTTCCCCCCCCCCCHHHHHHHHHGGGGCTTTTEEEEEEEEECHHHHHHCCCCCCCCHHHHHHHHHCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCEEEEETTTTCCTTTTHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCHHHHHHHHHHHHHHHHHC..TTTEEEEEEHHHHHCHHHHHHHHHHHCCCEEEEETTTTCCCCTTTTCCCCHHHHHHHHHHHHHCEEEEECTTTTCCCCCTTTTHHHHHHHHCEEEECCCEEEEETTTCCCEEEECCCCCCCHHHHHHHHHHCCCEEEEEHHHHHHCCCHHHHHHHHHHHHHHHHHHCCHHHHHHHCHHHHHHHHHHCHHHHHHHHCCTTTTC.... [Secondary structure assigned by YASARA]
1RSC-G  : .....LTY..DYTP.....KDTDLLAAFRFSPQ.....DEAGAAIAAESST..........TDMDRYKGKCYHIEP............FAFIAYPLDLFEE.......SVTNILTSIVGNVFGFKAIRSLRLEDIRFPVALVKTFQGPPHGIQVERDLLNKY....RPMLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKSQAETGEIKGHYLNVTAPTCEEMMKRAEFAKEL..........IIMHDFLTAGFTANTTLAKWCRGVLLHIHRAMHAVIDR...NHGIHFRVLAKCLRLSGGDHLH..............TLGFVDLMREDHIEA.FFTQDWASMPGVLPVASGGIHVWHMPALVEIF.GDDSVLQFGGGTLGHPWGNAPGATANRVALEACVQ...LREAGKWSPELAAALDLW................... [: RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (LARGE]
1GEH-B  : ..........GYEP.......RDIIAVFRVTPA.....EQAAGAVAAESST.GTWT..YEQERWADLSAKAYDFHD............IVRIAYPFHAFEE.......NLPGLLASIAGNIFGMKRVKGLRLEDLYFPEKLIREFDGPAFGIEGVRKMLEIK....RPIYGVVPKPKVGYSPEEFEKLAYDLLSNADYMKDDENLTSPWYNRFEERAEIMAKIIDKVENETGEKKTWFANITAD.LLEMEQRLEVLADL..........HAMVDVVITGWGALRYIRDLAAGLAIHGHRAMHAAFTR...YHGISMFVLAKLYRLIGIDQLH..............VIQNARILRESHYK...LEQKFYSIKAAFPTSSGGLHPGNIQPVIEAL.GTDIVLQLGGGTLGHPDGPAAGARAVRQAIDAIMQGIPLDEYAKTHKELARALEKW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE]
1SVD-A  : ......TY..EYTP.....LDSDILACFKITPQ.....EEAAAAVAAESSTG..........DMDYYKGRAYRIED............YAFIAYPIDLFEE.......SVVNVFTSLVGNVFGFKAVRGLRLEDVRFPLAYVKTCGGPPHGIQVERDKMNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFMRWRDRFLFVQDATETAEAQTGERKGHYLNVTAPTPEEMYKRAEFAKEI..........IIMHDYITGGFTANTGLAKWCQGVLLHIHRAMHAVIDR...NHGIHFRVLTKILRLSGGDHLH..............TLGWIDLLRESFIP..FFDQDWGSMPGVFAVASGGIHVWHMPALVNIF.GDDSVLQFGGGTLGHPWGNAAGAAANRVALEACVE...LTAAAQHSPELKIAMETW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE]
2YBV-A  : .......Y..DYTP.....KDTDILAAFRVTPQ.....EEAAAAVAAESSTG........LTDLDRYKGCCYDIEP............IAYIAYPLDLFEE.......SVTNMLTSIVGNVFGFKALKALRLEDLRIPVAYLKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKAQAETGEIKGHYLNVTAPTCEEMLKRAEFAKEL..........IIMHDFLTAGFTANTTLSKWCRGMLLHIHRAMHAVMDR...NHGIHFRVLAKCLRMSGGDHIH..............TLGFVDLLRENYIE..YFTQDWASMPGVMAVASGGIHVWHMPALVDIF.GDDAVLQFG.....HPWGNAPGATANRVALEACIQ...IREAARWSPELAAAC...................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN]
1BXN-C  : .....MGY..DYVP.....KDTDLLALFRITPQ.....VEAAAAVAGESST..WTV......ACDMYRAKAYRVDP............FCYVAYDLSLFEE.......SIANLTASIIGNVFSFKPIKAARLEDMRFPVAYVKTFAGPSTGIIVERERLDKF....RPLLGATTKPKLGLSGRNYGRVVYEGLKGLDFMKDDENINSQPFMHWRDRFLFVMDAVNKASAATGEVKGSYLNVTAGTMEEMYRRAEFAKSL..........IIMVD.LIVGWTCIQSMSNWCRDMILHLHRAGHGTYTR...NHGVSFRVIAKWLRLAGVDHMH..............VQGYYNVCRDAYTQ..FFDQDWASLRKVMPVASGGIHAGQMHQLIHLF.GDDVVLQFGGGTIGHPQGIQAGATANRVALEAMVL...LRDAARWCGPLRAALDTW................... [: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)]
1EJ7-L  : ......TY..EYQT.....KDTDILAAFRVTPQ.....EEAGAAVAAESSTGTWTTV.....SLDRYKGRCYRIER............IAYVAYPLDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENVNSQPFMRWRDRFLFCAEALYKAQAETGEIKGHYLNATAGTCEEMIKRAVFAREL..........IVMHDYLTGGFTANTSLAHYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHIH..............TLGFVDLLRDDFVE..YFTQDWVSLPGVLPVASGGIHVWHMPALTEIF.GDDSVLQFGGGTLGHPWGNAPGAVANRVALEACVK...IREACKWSPELAAACEVW................... [: RUBISCO (LARGE SUBUNIT)]
1IWA-C  : .....MGY..DYQV.....KDTDVLALFRVTPQ.....IEAAAAVAGESST...........AADLYRAKAYKVDQ............FAYIAYELDLFEE.......SIANLTASIIGNVFGFKAVKALRLEDMRLPLAYLKTFQGPATGVILERERLDKF....RPLLGCTTKPKLGLSGKNYGRVVYEALKGLDFVKDDENINSQPFMRWRERYLFTMEAVNKASAATGEVKGHYLNVTAATMEEMYARANFAKEL..........IIMID.LVIGYTAIQTMAKWARDMILHLHRAGNSTYSR...NHGMNFRVICKWMRMAGVDHIH..............TRGFYKTLLLPKLE..FFDMEWASLRKVMPVASGGIHAGQMHQLIHYLG.EDVVLQFGGGTIGHPDGIQAGATANRVALEAMIL...LREAAKTCGALRTALDLW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE]
1TEL-B  : ......GF.............QYLVLDYYLESV.....ETALAHFCSEQSTA........DEDFRVHAAKVIDYEV............RVTIAHPHCNFGP.......KIPNLLTAVCGETYFTPGVPVVKLMDIHFPDTYLADFEGPKFGIEGLRDILNAH....RPIFFGVVKPNIGLSPGEFAEIAYQSWLGLDIAKDDEMLADVTWSSIEERAAHLGKARRKAEAETGEPKIYLANITDE.VDSLMEKHDVAVRN..........ALLINALPVGLSAVRMLSNYT.QVPLIGHFPFIASFSR...KYGIHSKVMTKLQRLAGLDAVI..............VLENVIECTKP..........MGRIKPCLPVPGGSDSALTLQTVYEKVGNVDFGFVPGRGVFGHPMGPKAGAKSIRQAWEAIEQGISIETWAETHPELQAMVDQ.................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE, LARGE SUBUNIT]
2D69-A  : ......DF..NYEP.....GRDELIVEYYFEPN.....EEAAGRIASESSIGTW.........AKRSMAKVFYLEK............IAKIAYPLTLFEE.......SLVQLFSAVAGNVFGMKALKNLRLLDFHPPYEYLRHFKGPQFGVQGIREFMGVK....RPLTATVPKPKMGWSVEEYAEIAYELWSGIDLLKDDENFTSFPFNRFEERVRKLYRVRDRVEAETGETKEYLINITGP.VNIMEKRAEMVANE..........YVMIDIVVAGWSALQYMREVTEGLAIHAHRAMHAAFTR...RHGITMLALAKAARMIGVDQIH..............IKRINDFLLS...........WEHIRPVFPVASGGLHPGLMPELIRLF.GKDLVIQAGGGVMGHPDGPRAGAKALRDAIDAAIEGVDLDEKAKSSPELKKSLREV................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE]
2QYG-D  : ......GF.............NYIELDFDFECA.....HEAAAHLCSEQSTA...........RPRFAAKVLELSA............RVTIAHPHGNF........AKIPNLLSAVCGEVFFSPGIPLIRLQDIRFPEPYLAAFDGPRFGIAGVRERLQAF....RPIFFGVIKPNIGLPPQPFAELGYQSWTGLDIAKDDEMLADVDWCPLAERAALLGDACRRASAETGVPKIYLANITDE.VDRLTELHDVAVAN..........ALLINAMPVGLSAVRMLRKHA.TVPLIAHFPFIAAFSR...NYGIHSRVMTRLQRLAGFDVVI..............VLDCIRACLE...........MGPIKPCLPVPGGSDSAATLENVYRKVGSADFGFVPGRGVFGHPMGPAAGATSIRQAWDAIAAGIPVPDHAASHPELAAALRAF................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE-LIKE PROTEIN 2]
2V67-A  : .....LTY..DYVV......DTDILAAFRMTPQ.....EECGAAVAAESST...........SLDRYKGRCYDIEP............IAYVAYXIDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFVGXPHGIQVERDKLNKY....RGLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTXDDENVNSQPFMRWRDRFLFVAEAIYKAQAETGEVKGHYLNATAGTCEEMMKRAVXAKEL..........IIMHDYLTGGFTANTSLAIYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHLH..............ILGFVDLMRDDYVE..YFTQDWXSMPGVMPVASGGIHVWHMPALVEIF.GDDACLQFGGGTLGHPWGNAPGAAANRVALEACTQ...IRSACKWSPELAAACEVW................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN]
3NWR-A  : ....................EDTLEADYLIET......ARVADVMAGEQSSG............ARSRASVLRIEE............RITLSFPLANI.........NLPTLAATVAGNLYDLGEVTGVRLLSLRLPASYRARFELPRHGVAGTRALTDVK....RPMIGTIIKPNVGLSAAETAALVRELCEAVDFIXDDEVCANPAHAPLAERVRAVMSEVRRYRERSGRPVMVAFNITDD.LDAMRRHAELVERE..........CVMASINWCGFSAIQSLRRTT.PLVLHAHRNGYGMMSR...ALGMSFQAYQTLWRLSGVDHMH..............VIESARDCATP...............AVLPAFSSGQWAGTVQATFDAVRSTDLLFMSGGGILAHPDGPAAGVTSVRQAWAAVQAGTPLPVYAEHMPELRRALAFF................... [: A RUBISCO-LIKE PROTEIN]
3QFW-B  : ......................RIVATYHIAS......EQRALALAIEQSVEC............NIVGRVEDVAE............AVRIGLAAATAP.......AEPGQLLNMLFGNSSIQPD...IALADVELPAHYLTAFGGPRVGLAGIRTLTGAQ....RALTASALKP.QGLSPAALASIAHQLALGVDLIKDDHGLADQAFSPFAERAAAVGKAVREANAARGGRTLYAPNISG.TLDDMRRQLGVIRDE..........AVLVAPMIVGVSNFHAIVKEAAGLVVVAHPAMAGAA........IAAPLLGRLFRLFGADATV..............CLALAQAARD...........FGKLNACIPTPAGGIMLQRVNELLRFYG.QDVMLLI..........LTEQASRFVNKVADYGQR....................................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE]
uniref90: ......................RIIVTYQVAA......AARAEALAIEQSVEC............EIVGRVEAIAP............SVRVSLASATAP.......AEPGQLLNMLFGNSSIQPD...VTLADVELPPAYPAAFGGPKLGISGLRAKLGAP....RALTGSALKP.QGLAPEALAGLAHRLALGVDLIKDDHGIADQAFSPFAARVPAVARAMREACAVRGAAMLYAPHVSG.SLDDMRRQLDIVRRE..........VVMLMPMIVGLANFHLIAKEAEGLIVLAHPSLAGAQ........IAPDLLGKLFRLLGADATI..............CRALADAARR...........WHDLKPCLPVPAGGIAIDRIKELLAFYG.TDVMLLI..........LTEHAARFTAEVASHGQ........................................ [uniref90|Q6N7T7 Ribulose bisphosphate carboxylase-like protein 1 n=2 Tax=Rhodopseudomonas palustris RepID=RBLL1_RHOPA]
2ZVI-A  : ......................ELLATYLLT.......EKKAEQIATGLTVG...........MQKHKGRVIKVEE............VITIAYPEINFSQ.......DIPALLTTVFGKLSL...DGKIKLIDLHFSEAFKRALPGPKFGVYGIRKLLGE.....RPLLMSIFKGVIGRDLSDIKEQLRQQALGVDLIKDDEIFFETGLAPFETRIAEGKQILKETYEQTGHKTLYAVNLTGR.TADLKDKARRAAEL..........ALLFNVFAYGLDVMQGLAED..PVPIMAHPAVSGAFTS...FYGFSHALLGKLNRYCGADFSL..............ALAIHEECVR.............AFNQTFAVPSAGIHPGMVPLLMRDF.GIDHIINAGGGVHGHPNGAQGGGRAFRAIIDAVLEAQPIDEKAEQCKDLKLALDKWGK................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE]
uniref90: ......................................HKQAKIIAVGQTAG...........LRQHLAEVIEIKT..............KIRFPEINVEN.......DLASLLTMIFGKYSM...AGAAKVIGVHLPESYGQR...PKFGITGIRKILNV.....RPLIMAIFKPALGLSAADHAVILKQVADALDIIKDDEILGDLETAPTLKRLEACRQVLEAIKQQTGRTVLYAVNVTGK.ADKLIEKARLLVKE..........ALLLNVLTYGFSVLEALAAD..NVPIFAHPAFAGAMCA...DTGLSYSVIGRFMAHGGVDAVL..............EKKIRDSLRS.............VF....PVPSAGIHPGIVPKAIADY.GDDVILNAGTGIMDHPNNPGAGVKAFFEALERVKTGQSFTLDTVPEGALKQALQKWG.................. [uniref90|B7KIK8 Ribulose-bisphosphate carboxylase n=1 Tax=Cyanothece sp. PCC 7424 RepID=B7KIK8_CYAP7]
2OEK-B  : ......................AVMATYLLHDE.....RKKAEGIALGLTIG...........LRKHKGEVVAIEE............IVKIAYPTVNFSA.......DLPALLVTTFGKLSLD...GEVRLLDLEFPDEWKRQFPGPRFGIDGIRDRVGVH....RPLLMSIFKGMIGRDLAYLTSELKKQALGVDLVXDDEILFDSELLPFEKRITEGKAALQEVYEQTGKRTLYAVNLTGK.TFALKDKAKRAAEL..........VLLFNVFAYGLDVLQALRED..AVPIMAHPAFSGAVTP...FYGVAPSLWGKLLRLAGADFVL..............ALGIARALTD.............PFARAFPVPSAGIHPGLVPLIIRDF.GLDTIVNAGGGIHGHPDGAIGGGRAFRAAIDAVLAGRPLRAAAAENEALQKAIDRWGV................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE ENOLASE]
uniref90: .......................VIATYRLAGG.....TKKAETIALGMTVG...........LQRHAGRVVSVDA............LIRIAYPLANLTP.......DLPSLLTATFGKLSMD...GKIRLLDLTLPPTFAAAFPGPKLGVEGIRERLGVH....RPLLMSIFKSCVGLTLAELAEGFFQQALGVDLIKDDEIFFNDTDAPFEQRLEACLQATERARRETGQTVLYAINLTGP.VHRLPEKARRAARL..........ALLINVLPYGFDLLQRLAED..TVPLIAHPALAGALYP...DYGIAAPLLGTLMRLAGADLVL..............ALGLASRLTD.............PHRPTFPVPSAGIHPGLVPHMMDDF.GLDVVINAGGGIHGHPGGAAAGGRAFRAAIAAGVGGVPLEQAAAGSRDLRAALDQWG.................. [uniref90|D5MLU6 2,3-diketo-5-methylthiopentyl-1-phosphate enolase (DK-MTP-1-P enolase) n=1 Tax=NC10 bacterium 'Dutch sediment' RepID=D5MLU6_9BACT]
3FK4-A  : ......................GIIATYLIHDD.....EKKAEQIALGLTIG...........LKQHKGNVIHVEE............IIKIEYPLLNFSP.......DLPAILTTTFGKLSLD...GEVKLIDLTFSDELKKHFPGPKFGIDGIRNLLQVH....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENALTPLTKRIVSGKEVLQSVYETYGHKTLYAVNLTGR.TFDLKENAKRAVQA..........ILLFNVFAYGLDVLQSLAED..PVPIMAHPAVSGAYSA...LYGVSSPLLGKLLRYAGADFSL..............ALAISKYLTE...........DASFKKSFSVPSAGIHPGFVPFIVRDF.GKDVVINAGGGIHGHPNGAQGGGKAFRTAIDATLQNKPLHEV..DDINLHSALQIWG.................. [: RUBISCO-LIKE PROTEIN]
uniref90: ......................GIIATYLIHDD.....EKKAEQIALGLTIG...........LKQHKGNVLHVEE............IIKIEYPLLNFSP.......DLPAILTTTFGKLSLD...GEVKLIDLTFSDELKKHFPGPKFGIDGIRNLLQVH....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENALTPLTNRIVSGKEVLQSVYETYGHKTLYAVNVTGR.TFDLKENAKRAVQA..........ILLFNVFAYGLDVLQSLAED..PVPIMAHPAVSGAYSA...LYGISSPLLGKLLRYAGADFSL..............ALAISKYLTE...........DVFFKKSFSVPSAGIHPGFVPFIIRDF.GKDVVINAGGGIHGHPNGAQGGGKAFRTAIDATLQNKPLHEV..DDINLHSALQIWG.................. [uniref90|C3P745 2,3-diketo-5-methylthiopentyl-1-phosphate enolase n=71 Tax=Bacillus cereus group RepID=MTNW_BACAA]

NOTE: To save space, only 20 of 1110 template profile alignments are shown above. The complete set of alignments can be found in the file Homology_5han-~_profile.ali. The template profile contains structural alignments of 16 PDB files, which provide safe anchors for the remaining sequence-based alignments (only reliable regions shown).

In the alignment above, 448 of 470 target residues (95.3%) are aligned to template residues. Among these aligned residues, the sequence identity is 64.1% and the sequence similarity is 75.9% ('similar' means that the BLOSUM62 score is > 0). The following 6 loops had to be modeled (only the first of 2 similar loops in the homodimer is listed):

LoopN-terminal anchorLoop sequenceC-terminal anchor
1MDQSNRYANLN
3SNRYANLNLKEED
5LETFAKYNSASHV
7KLIPAKGHGFLEV
9EIDETAFGDDPVKGGGLFKV
11WREKLGVHKNone

After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).

The resulting half-refined model has been saved as Homology_5han-~04_refined050.yob and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals0.249Optimal
Packing 1D-0.840Good
Packing 3D-1.247Satisfactory
Overall-0.872Good

Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as Homology_5han-~04_refined100.yob, the corresponding Z-scores are listed below:

Check typeQuality Z-scoreComment
Dihedrals0.469Optimal
Packing 1D-0.473Good
Packing 3D-1.322Satisfactory
Overall-0.731Good

Since the overall quality Z-score improved to -0.731 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.

NOTE: 8 residues contained in N- and C-terminal unaligned tails of the homodimeric model have been excluded from the Z-scores in both tables above, since they are not reliable (YASARA does not yet perform ab initio structure prediction) and would have mainly added noise to the result.

The final model for this template and alignment has been saved as Homology_5han-~04.yob, and is shown below, together with a plot of its overall quality Z-score, shown per residue:

6.12. Homology model 12/15, based on template 5HJX-~, alignment variant 01

This model is a homodimer, and based on the following profile-profile alignment:

(To improve readability, only up to ten lines of the complete target multiple sequence alignment (MSA) shown above are also displayed here (upside down). The template MSA has been shrunk and focused on structurally aligned PDB entries. The actual target-template alignment can be found in the middle at the line named 'Match'.)

Q08EW6  : .......................................................................................................................NNQGGGDIEHAKIHGIYMPERAIQLFDGPSKDISDMWRILGRPVKDGGYNAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEIQGNQVFSPMNQTIPLVVDAMKRAQDETGQAKLFSANITADDQYEMCARADFILEAFGP..DADKVAFLVDGYVGDPGMITTARSQYPNQYLHYHRAGHGAVNSPKIKRGYTAFVLAKMSRLQGASGAHVGTMGYGKME................................................................................................................................ [uniref90|Q08EW6 Ribulose 1,5-bisphosphate carboxylase/oxygenase large subunit (Fragment) n=1 Tax=uncultured marine bacterium RepID=Q08EW6_9BACT]
Q5DVV5  : ............................................................................................................................................................................IIKPKLGLRPKPFAEACYNFWLGGDFIKNDEPQGNQIWGPIKEVVPLVKDSLVRAQDDTGMAKLFSFNITADDHYEMLHRGEYILETFAEFSE..NIAFLVDGCVGGPGMVTTARRNFPDQFLHYHRAGHGAVTSDQSDRGYNMLVHMKMARLQGASGIHTGTMGYGKMEGAADDKVIAYMLERDSADGLSYHQEWEGMKATTPIICGGMNA...................................................................................... [uniref90|Q5DVV5 Ribulose-1,5-bisphosphate carboxylase oxygenase large subunit (Fragment) n=11 Tax=uncultured prokaryote RepID=Q5DVV5_9ZZZZ]
Q933G7  : ........................................................................................................................................VPPAYLRLFDGPSTTIKDLWRVLGRPVVDGGFIVGTIIKPKLGLRPQPFADACYDFWLGGDFIKNDEPQGNQVFAPFKDTVRAVNDAMRRAQDATGQPKLFSFNITADDHYEMLARGEYILETFGE..NADHVAFLVDGYVAGPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHVGTMGYGKMEGEASDRDSAFMITQDSAEGPYFKQEW...................................................................................................... [uniref90|Q933G7 Form II ribulose 1,5-bisphosphate carboxylase/oxygenase (Fragment) n=5 Tax=Rhodopseudomonas palustris RepID=Q933G7_RHOPA]
F2ZCE9  : .....................................................................................................................................DFYVPPDFLRLFDGPATTISNLWRVLGRPHQNGGFIVGTIVKPKLGLRPRPFADACYDFWLGGDFIKNDEPQGNQTFSPLKETIPLVADAMRRAQDETGEAKLFSANITADDHYEMVARGEFILDTFGEF..ADHVAFLVDGYVAGAAAVTTARRSFPQQYLHYHRAGHGAITSPQSKRGYTAFVHCKMARLQGASGIHTGTMSFGKMEGEAADRAIAFMLEQDSADGPYFHQEWHGMNPTTSIISG.......................................................................................... [uniref90|F2ZCE9 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=1 Tax=uncultured bacterium RepID=F2ZCE9_9BACT]
F2ZCD0  : ......................................................................................................................GNNQGMGDIANAQMQDFYVPPAMLALFDGPAKSINDLWTLLGRDNENGGYIAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEPQGNQVFCPLKKVLPLVHDAMKRAQDETGEAKLFSLNITADDHYEMCARADFGLETFGE..DAPRLAFLVDGFVGGPGMVTTARRQYSSQYLHYHRAGHGMITSPSSKRGYTAYILAKMSRLMGASGIHVGTMGYGKMEGGADDKIIAYMIERDECQGPFYYQKWHGMKPTTPIVSGGM........................................................................................ [uniref90|F2ZCD0 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=4 Tax=uncultured bacterium RepID=F2ZCD0_9BACT]
F5BZE6  : ......................................................................................................................GNNQGMGDVEYAKMIDFYMARSLLTLFDGPAMNITDMWRVLGRPQVNGGMVVGTIIKPKLGLRPKPFADACYMFWMGGDFIKNDEPQGNQVFAPTREIIPLVAEAMERAQQETGEAKIFSANITADDPFEMIRRGEFILEAFGK..NASHVAFLVDGYVGGPSAVTLCRRYFPNQFLHYHRAGHGAVTSNQSKRGYTVLTHMKMSRLQGASGIHTGTMGYGKMEGDKNEKMVAYMIERDEAMGVYYNQPWHGMTATTPIISGGMNALR.................................................................................... [uniref90|F5BZE6 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II (Fragment) n=1 Tax=alpha proteobacterium LM-5 RepID=F5BZE6_9PROT]
Q9FPW1  : LDQSSRYADLSLDEATLVKNGKHVLVAYIMKPKAGYDYLATAAHFAAESSTGTNVNVCTTDDFTKSVDALVYYIDPDSEE.........MKIAYPTLLFDRNIIDGRGMMCSFLTLAIGNNQGMGDVEYGKIYDFYLPPSFLRLYDGPAVNVEDMWRILGKGTSNGGLVDGTIIKPKLGLQPNPFGEACYSFWQGGDFIKNDEPQGNQVFCQMNECIPEVVKAMRACVKETGSSKLFSANITADDPEEMIARGKYIMSQFGPLSE..NCAFLVDGYVAGGTAVTCCRRNFPKQFLHYHRAGHGSVTSPQTQRGYTAFVHTKISRVIGASGIHVGTMSFGKMEGDASDKNIAYMLQDDEADGPYYRQEWQGMKETTPIISGGMNALRLPAFFENLGHSNVILTAGGGSFGHKDGPKIGAISCRQGEEAWKSLSDVIEYAKTHEEIKGAFLTFQKDADQIYPGWKEKLG... [uniref90|Q9FPW1 Ribulose 1,5-bisphosphate carboxylase oxygenase large subunit n=1 Tax=Symbiodinium sp. RepID=Q9FPW1_SYMSP]
E6VVI6  : .DQTSRYVNFDLKEDQLIADGNHVLCAYIYKPANGYGNVEVAAHFAAESSTGTNVEVCTTDDFTKGVDALVYEVSDASNGDS......LMKIAYPVELFDRNIIDGRAMLASFLTLCIGNNQGMGDVAYAKMHDFYVPRQYLELFDGPSKNIADFWRMLGRPTENGGMIAGTIVKPKLGLRPKPFADACYHFWLGGDFVKNDEPQGNQVFAPLKETITAVADAMRRAQDETGEAKIFSANITADDPREMIARGEFILNAFGE..NASRVAFLVDGYVAGPTAITTARRNFPNQFLHYHRAGHGAVTSPQAKRGYTAFVLSKMSRLQGASGIHTGTMGFGKMEGEMADKSMAYMIEREEAQGPYFKQKWYGMKATTPMISGGMNALRLPGFFDNLGHSNICQTSGGGAFGHLDGPTAGALSLRQSHDAWIQGVNLLDYAKEHNELARAFESFPGDADRFYPTWRHQL.... [uniref90|E6VVI6 Ribulose-bisphosphate carboxylase n=1 Tax=Desulfovibrio aespoeensis Aspo-2 RepID=E6VVI6_DESAO]
Q8RTI1  : MDQSNRYADLSLKEDDLIKGGNHVLVAYLMKPKTGYGYLEAAAHFSAESSTGTNVEVSTTDDFTKGVDALVYEIDEAK.........EIMKIAYPVDLFDRNITDGRAMIVSFLTLAIGNNQGMGDIAYAKMLDFYVPQKYLRLFDGPSKDISDLWRILGRPVVNGGYIAGTIIKPKLGLRPKPFAEAAYQFWLGGDFIKNDEPQGNQVFSPMRETIPLVYDSMKRAMDETGEAKLFSANITADDHYEMMARGEFILNTFGP..DADKVAFLVDGYVGGPGMVTTARRHFANQYLHYHRAGHGAVTSPSAKRGYTAFVLAKMSRLQGASGIHVGTMGYGKMEGDATDKNIAYMIERDSADGPFYHQEWYGMKPTTPIISGGMNALRLPGFFENLGHANLINTSGGGSYGHIDSPAAGAISLRQAYECWQQGADPIEFAKEHKEFARAFESFPGDADTIFPGWREKLGVHK [uniref90|Q8RTI1 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II n=1 Tax=magnetite-containing magnetic vibrio RepID=Q8RTI1_9PROT]
Q0F2Z8  : MDQSNRYADLSLNEADLIAGGKHLLVAYKLIPAKGYGFLEVAAHIAAESSTGTNVEVSTTDDFTRGVDALVYDIDETAFGDEGVTGGGLMKVAYPVELFDPNLIDGHYNVSHMWSLILGNNQGMGDHEGLRMLDFMVPECMIRKFDGPSAGIADLWKVLGRPEVDGGYISGTIIKPKLGLRPEPFAKACLDFWLGGDFIKNDEPQANQPFCPMKVVIPKVAEAMDRAQQETGQAKLFSANATADYHGECVARGEYILSEFAKYGNEKHVAFLIDGFVTGPAGVTTARRAFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLARLQGASGIHTGTMGYGKMEGHGKETVLAYMLERDECMGHYFNQKWYGMKPTAPIISGGMNALRLPGFFENLGHGNVINTCGGGSFGHIDSPAAGGKSLDQAYDCWKSGTDPIEYAKTHGEFARAFESFPGDADKLYPGWRDKLGVHK [uniref90|Q0F2Z8 Ribulose-bisphosphate carboxylase n=1 Tax=Mariprofundus ferrooxydans PV-1 RepID=Q0F2Z8_9PROT]
SecStr  : CCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCEEECCCCCCHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCEEEECCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEECCCCCCHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCHHCCCCCCCEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHHHHCCCC [Secondary structure predicted by PsiPred]
Target  : MDQSNRYANLNLKEEDLIKNGKHLLVAYKLIPAKGHGFLEVAAHVAAESSTGTNVEVSTTDDFTRGVDALVYEIDETAFGDDPVKGGGLFKVAYPVELFDPNLTDGTYNISHMWSLILGNNQGMGDHQGLRMLDFLVPEMMVRKFDGPSANISNLWKVLGRSETDGGYIAGTIIKPKLGLRPEPFAKACYDFWLGGDFIKNDEPQANQPFCPMEVVMPKVAEAMDRAQQATGQAKLFSANITADYYKEMIHRGDFVLETFAKYNSASHVAFLVDGFVTGPAGVTTARREFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLVRLMGASGMHTGTMGYGKMEGHGKETVLAYMLERDECQGPYFYQKWYGMKATTPIISGGMNALRLPGFFQNLGHGNVINTCGGGAFGHIDSPAAGGISLGQAYDCWKSGSDPIEYAKTHKEFARAFESFPKDGDKLFAGWREKLGVHK
Match   : MDQSNRYANLNLKE:|LI :G|H:L AY | P    :F||:AAH :AESSTGTNVEVSTTDDFTRGVDALVYE|DE:          :L:K|AYP|ELFD N: DG   I: : :L |GNNQGMGD |  |M DF VP   :| FDGPS::I::LW|VLGR   :GG|I:GTIIKPKLGLRP|PFA:ACYDFWLGGDFI:NDEPQ:NQ F:P:: ::  VA|AM RAQ: TG|AKLFS NITAD | EM| RG|F|LETFA   :A:H|AFLVDG|V:GPA:VTTARR FP  |LH|HRAGHGAVTS :S  G   :   K|:RL:GASG:HTGTMG|GKMEG:: | :|AYM| :D ::GPYF|Q:W GM: TTPIISGGMNALR|PGFF:NLGH:N:I T:GGGAFGH|D: AAG: SL QA :CWK:G:DP|E|AK H|EFARAFESFP:D:DKL| :WR KL    
Template: MDQSNRYANLNLKESELIAGGRHVLCAYIMKPK...NFIQTAAHFVAESSTGTNVEVSTTDDFTRGVDALVYEVDEA..........SLMKIAYPIELFDRNVIDGRAMIASFLTLTIGNNQGMGDVEYAKMYDFYVPPAYLKLFDGPSTTIKDLWRVLGRPVINGGFIVGTIIKPKLGLRPQPFANACYDFWLGGDFIXNDEPQGNQVFAPFKDTVRAVADAMRRAQDKTGEAKLFSFNITADDHYEMLARGEFILETFAD..NADHIAFLVDGYVAGPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHTGTMGFGKMEGEAADRAIAYMITEDAADGPYFHQEWLGMNPTTPIISGGMNALRMPGFFDNLGHSNLIMTAGGGAFGHVDGGAAGAKSLRQAEQCWKQGADPVEFAKDHREFARAFESFPQDADKLYPNWRAKL....
SecStr  : CCHHHHHCTTTTHHHHHHHHCCCEEEEEEEECC...HHHHHHHHHHHHCCCCCCCCTTTTHHHHHHCCCEEEEEETT..........EEEEEEETTTTCCCCCCCCCCCHHHHHHHHHGGGGCTTTTEEEEEEEEECHHHHHHCCCCCCCCHHHHHHHHHCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCEEEEETTTTCCTTTTHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCHHHHHHHHHHHHHHHHHC..TTTEEEEEEHHHHHCHHHHHHHHHHHCCCEEEEETTTTCCCCTTTTCCCCHHHHHHHHHHHHHCEEEEECTTTTCCCCCTTTTHHHHHHHHCEEEECCCEEEEETTTCCCEEEECCCCCCCHHHHHHHHHHCCCEEEEEHHHHHHCCCHHHHHHHHHHHHHHHHHHCCHHHHHHCCHHHHHHHHHHCHHHHHHHHCTTTTCC.... [Secondary structure assigned by YASARA]
1RSC-G  : ....LTYYTPDYTP.....KDTDLLAAFRFSPQ.....DEAGAAIAAESST..........TDMDRYKGKCYHIEP............FAFIAYPLDLFEE.......SVTNILTSIVGNVFGFKAIRSLRLEDIRFPVALVKTFQGPPHGIQVERDLLNKY....RPMLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKSQAETGEIKGHYLNVTAPTCEEMMKRAEFAKEL..........IIMHDFLTAGFTANTTLAKWCRGVLLHIHRAMHAVIDR...NHGIHFRVLAKCLRLSGGDHLH..............TLGFVDLMREDHIEA.FFTQDWASMPGVLPVASGGIHVWHMPALVEIF.GDDSVLQFGGGTLGHPWGNAPGATANRVALEACVQ...LREAGKWSPELAAALDLW................... [: RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (LARGE]
1GEH-B  : ..........GYEP.......RDIIAVFRVTPA.....EQAAGAVAAESST.GTWT..YEQERWADLSAKAYDFHD............IVRIAYPFHAFEE.......NLPGLLASIAGNIFGMKRVKGLRLEDLYFPEKLIREFDGPAFGIEGVRKMLEIK....RPIYGVVPKPKVGYSPEEFEKLAYDLLSNADYMKDDENLTSPWYNRFEERAEIMAKIIDKVENETGEKKTWFANITAD.LLEMEQRLEVLADL..........HAMVDVVITGWGALRYIRDLAAGLAIHGHRAMHAAFTR...YHGISMFVLAKLYRLIGIDQLH..............VIQNARILRESHYK...LEQKFYSIKAAFPTSSGGLHPGNIQPVIEAL.GTDIVLQLGGGTLGHPDGPAAGARAVRQAIDAIMQGIPLDEYAKTHKELARALEKW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE]
1SVD-A  : .....TYWMPEYTP.....LDSDILACFKITPQ.....EEAAAAVAAESSTG..........DMDYYKGRAYRIED............YAFIAYPIDLFEE.......SVVNVFTSLVGNVFGFKAVRGLRLEDVRFPLAYVKTCGGPPHGIQVERDKMNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFMRWRDRFLFVQDATETAEAQTGERKGHYLNVTAPTPEEMYKRAEFAKEI..........IIMHDYITGGFTANTGLAKWCQGVLLHIHRAMHAVIDR...NHGIHFRVLTKILRLSGGDHLH..............TLGWIDLLRESFIP..FFDQDWGSMPGVFAVASGGIHVWHMPALVNIF.GDDSVLQFGGGTLGHPWGNAAGAAANRVALEACVE...LTAAAQHSPELKIAMETW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE]
2YBV-A  : ......YYTPDYTP.....KDTDILAAFRVTPQ.....EEAAAAVAAESSTG........LTDLDRYKGCCYDIEP............IAYIAYPLDLFEE.......SVTNMLTSIVGNVFGFKALKALRLEDLRIPVAYLKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKAQAETGEIKGHYLNVTAPTCEEMLKRAEFAKEL..........IIMHDFLTAGFTANTTLSKWCRGMLLHIHRAMHAVMDR...NHGIHFRVLAKCLRMSGGDHIH..............TLGFVDLLRENYIE..YFTQDWASMPGVMAVASGGIHVWHMPALVDIF.GDDAVLQFG.....HPWGNAPGATANRVALEACIQ...IREAARWSPELAAAC...................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN]
1BXN-C  : ....MGYWDGDYVP.....KDTDLLALFRITPQ.....VEAAAAVAGESST..WTV......ACDMYRAKAYRVDP............FCYVAYDLSLFEE.......SIANLTASIIGNVFSFKPIKAARLEDMRFPVAYVKTFAGPSTGIIVERERLDKF....RPLLGATTKPKLGLSGRNYGRVVYEGLKGLDFMKDDENINSQPFMHWRDRFLFVMDAVNKASAATGEVKGSYLNVTAGTMEEMYRRAEFAKSL..........IIMVD.LIVGWTCIQSMSNWCRDMILHLHRAGHGTYTR...NHGVSFRVIAKWLRLAGVDHMH..............VQGYYNVCRDAYTQ..FFDQDWASLRKVMPVASGGIHAGQMHQLIHLF.GDDVVLQFGGGTIGHPQGIQAGATANRVALEAMVL...LRDAARWCGPLRAALDTW................... [: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)]
1EJ7-L  : .....TYYTPEYQT.....KDTDILAAFRVTPQ.....EEAGAAVAAESSTGTWTTV.....SLDRYKGRCYRIER............IAYVAYPLDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENVNSQPFMRWRDRFLFCAEALYKAQAETGEIKGHYLNATAGTCEEMIKRAVFAREL..........IVMHDYLTGGFTANTSLAHYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHIH..............TLGFVDLLRDDFVE..YFTQDWVSLPGVLPVASGGIHVWHMPALTEIF.GDDSVLQFGGGTLGHPWGNAPGAVANRVALEACVK...IREACKWSPELAAACEVW................... [: RUBISCO (LARGE SUBUNIT)]
1IWA-C  : ....MGYWNPDYQV.....KDTDVLALFRVTPQ.....IEAAAAVAGESST...........AADLYRAKAYKVDQ............FAYIAYELDLFEE.......SIANLTASIIGNVFGFKAVKALRLEDMRLPLAYLKTFQGPATGVILERERLDKF....RPLLGCTTKPKLGLSGKNYGRVVYEALKGLDFVKDDENINSQPFMRWRERYLFTMEAVNKASAATGEVKGHYLNVTAATMEEMYARANFAKEL..........IIMID.LVIGYTAIQTMAKWARDMILHLHRAGNSTYSR...NHGMNFRVICKWMRMAGVDHIH..............TRGFYKTLLLPKLE..FFDMEWASLRKVMPVASGGIHAGQMHQLIHYLG.EDVVLQFGGGTIGHPDGIQAGATANRVALEAMIL...LREAAKTCGALRTALDLW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE]
1TEL-B  : .....GFFAS...........QYLVLDYYLESV.....ETALAHFCSEQSTA........DEDFRVHAAKVIDYEV............RVTIAHPHCNFGP.......KIPNLLTAVCGETYFTPGVPVVKLMDIHFPDTYLADFEGPKFGIEGLRDILNAH....RPIFFGVVKPNIGLSPGEFAEIAYQSWLGLDIAKDDEMLADVTWSSIEERAAHLGKARRKAEAETGEPKIYLANITDE.VDSLMEKHDVAVRN..........ALLINALPVGLSAVRMLSNYT.QVPLIGHFPFIASFSR...KYGIHSKVMTKLQRLAGLDAVI..............VLENVIECTKP..........MGRIKPCLPVPGGSDSALTLQTVYEKVGNVDFGFVPGRGVFGHPMGPKAGAKSIRQAWEAIEQGISIETWAETHPELQAMVDQ.................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE, LARGE SUBUNIT]
2D69-A  : .....DFVDLNYEP.....GRDELIVEYYFEPN.....EEAAGRIASESSIGTW.........AKRSMAKVFYLEK............IAKIAYPLTLFEE.......SLVQLFSAVAGNVFGMKALKNLRLLDFHPPYEYLRHFKGPQFGVQGIREFMGVK....RPLTATVPKPKMGWSVEEYAEIAYELWSGIDLLKDDENFTSFPFNRFEERVRKLYRVRDRVEAETGETKEYLINITGP.VNIMEKRAEMVANE..........YVMIDIVVAGWSALQYMREVTEGLAIHAHRAMHAAFTR...RHGITMLALAKAARMIGVDQIH..............IKRINDFLLS...........WEHIRPVFPVASGGLHPGLMPELIRLF.GKDLVIQAGGGVMGHPDGPRAGAKALRDAIDAAIEGVDLDEKAKSSPELKKSLREV................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE]
2QYG-D  : .....GFYAK...........NYIELDFDFECA.....HEAAAHLCSEQSTA...........RPRFAAKVLELSA............RVTIAHPHGNF........AKIPNLLSAVCGEVFFSPGIPLIRLQDIRFPEPYLAAFDGPRFGIAGVRERLQAF....RPIFFGVIKPNIGLPPQPFAELGYQSWTGLDIAKDDEMLADVDWCPLAERAALLGDACRRASAETGVPKIYLANITDE.VDRLTELHDVAVAN..........ALLINAMPVGLSAVRMLRKHA.TVPLIAHFPFIAAFSR...NYGIHSRVMTRLQRLAGFDVVI..............VLDCIRACLE...........MGPIKPCLPVPGGSDSAATLENVYRKVGSADFGFVPGRGVFGHPMGPAAGATSIRQAWDAIAAGIPVPDHAASHPELAAALRAF................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE-LIKE PROTEIN 2]
2V67-A  : ....LTYYTPDYVV......DTDILAAFRMTPQ.....EECGAAVAAESST...........SLDRYKGRCYDIEP............IAYVAYXIDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFVGXPHGIQVERDKLNKY....RGLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTXDDENVNSQPFMRWRDRFLFVAEAIYKAQAETGEVKGHYLNATAGTCEEMMKRAVXAKEL..........IIMHDYLTGGFTANTSLAIYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHLH..............ILGFVDLMRDDYVE..YFTQDWXSMPGVMPVASGGIHVWHMPALVEIF.GDDACLQFGGGTLGHPWGNAPGAAANRVALEACTQ...IRSACKWSPELAAACEVW................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN]
3NWR-A  : ....................EDTLEADYLIET......ARVADVMAGEQSSG............ARSRASVLRIEE............RITLSFPLANI.........NLPTLAATVAGNLYDLGEVTGVRLLSLRLPASYRARFELPRHGVAGTRALTDVK....RPMIGTIIKPNVGLSAAETAALVRELCEAVDFIXDDEVCANPAHAPLAERVRAVMSEVRRYRERSGRPVMVAFNITDD.LDAMRRHAELVERE..........CVMASINWCGFSAIQSLRRTT.PLVLHAHRNGYGMMSR...ALGMSFQAYQTLWRLSGVDHMH..............VIESARDCATP...............AVLPAFSSGQWAGTVQATFDAVRSTDLLFMSGGGILAHPDGPAAGVTSVRQAWAAVQAGTPLPVYAEHMPELRRALAFF................... [: A RUBISCO-LIKE PROTEIN]
3QFW-B  : ......................RIVATYHIAS......EQRALALAIEQSVEC............NIVGRVEDVAE............AVRIGLAAATAP.......AEPGQLLNMLFGNSSIQPD...IALADVELPAHYLTAFGGPRVGLAGIRTLTGAQ....RALTASALKP.QGLSPAALASIAHQLALGVDLIKDDHGLADQAFSPFAERAAAVGKAVREANAARGGRTLYAPNISG.TLDDMRRQLGVIRDE..........AVLVAPMIVGVSNFHAIVKEAAGLVVVAHPAMAGAA........IAAPLLGRLFRLFGADATV..............CLALAQAARD...........FGKLNACIPTPAGGIMLQRVNELLRFYG.QDVMLLI..........LTEQASRFVNKVADYGQR....................................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE]
uniref90: ......................RIIVTYQVAA......AARAEALAIEQSVEC............EIVGRVEAIAP............SVRVSLASATAP.......AEPGQLLNMLFGNSSIQPD...VTLADVELPPAYPAAFGGPKLGISGLRAKLGAP....RALTGSALKP.QGLAPEALAGLAHRLALGVDLIKDDHGIADQAFSPFAARVPAVARAMREACAVRGAAMLYAPHVSG.SLDDMRRQLDIVRRE..........VVMLMPMIVGLANFHLIAKEAEGLIVLAHPSLAGAQ........IAPDLLGKLFRLLGADATI..............CRALADAARR...........WHDLKPCLPVPAGGIAIDRIKELLAFYG.TDVMLLI..........LTEHAARFTAEVASHGQ........................................ [uniref90|Q6N7T7 Ribulose bisphosphate carboxylase-like protein 1 n=2 Tax=Rhodopseudomonas palustris RepID=RBLL1_RHOPA]
2ZVI-A  : ......................ELLATYLLT.......EKKAEQIATGLTVG...........MQKHKGRVIKVEE............VITIAYPEINFSQ.......DIPALLTTVFGKLSL...DGKIKLIDLHFSEAFKRALPGPKFGVYGIRKLLGE.....RPLLMSIFKGVIGRDLSDIKEQLRQQALGVDLIKDDEIFFETGLAPFETRIAEGKQILKETYEQTGHKTLYAVNLTGR.TADLKDKARRAAEL..........ALLFNVFAYGLDVMQGLAED..PVPIMAHPAVSGAFTS...FYGFSHALLGKLNRYCGADFSL..............ALAIHEECVR.............AFNQTFAVPSAGIHPGMVPLLMRDF.GIDHIINAGGGVHGHPNGAQGGGRAFRAIIDAVLEAQPIDEKAEQCKDLKLALDKWGK................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE]
uniref90: ......................................HKQAKIIAVGQTAG...........LRQHLAEVIEIKT..............KIRFPEINVEN.......DLASLLTMIFGKYSM...AGAAKVIGVHLPESYGQR...PKFGITGIRKILNV.....RPLIMAIFKPALGLSAADHAVILKQVADALDIIKDDEILGDLETAPTLKRLEACRQVLEAIKQQTGRTVLYAVNVTGK.ADKLIEKARLLVKE..........ALLLNVLTYGFSVLEALAAD..NVPIFAHPAFAGAMCA...DTGLSYSVIGRFMAHGGVDAVL..............EKKIRDSLRS.............VF....PVPSAGIHPGIVPKAIADY.GDDVILNAGTGIMDHPNNPGAGVKAFFEALERVKTGQSFTLDTVPEGALKQALQKWG.................. [uniref90|B7KIK8 Ribulose-bisphosphate carboxylase n=1 Tax=Cyanothece sp. PCC 7424 RepID=B7KIK8_CYAP7]
2OEK-B  : ......................AVMATYLLHDE.....RKKAEGIALGLTIG...........LRKHKGEVVAIEE............IVKIAYPTVNFSA.......DLPALLVTTFGKLSLD...GEVRLLDLEFPDEWKRQFPGPRFGIDGIRDRVGVH....RPLLMSIFKGMIGRDLAYLTSELKKQALGVDLVXDDEILFDSELLPFEKRITEGKAALQEVYEQTGKRTLYAVNLTGK.TFALKDKAKRAAEL..........VLLFNVFAYGLDVLQALRED..AVPIMAHPAFSGAVTP...FYGVAPSLWGKLLRLAGADFVL..............ALGIARALTD.............PFARAFPVPSAGIHPGLVPLIIRDF.GLDTIVNAGGGIHGHPDGAIGGGRAFRAAIDAVLAGRPLRAAAAENEALQKAIDRWGV................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE ENOLASE]
uniref90: .......................VIATYRLAGG.....TKKAETIALGMTVG...........LQRHAGRVVSVDA............LIRIAYPLANLTP.......DLPSLLTATFGKLSMD...GKIRLLDLTLPPTFAAAFPGPKLGVEGIRERLGVH....RPLLMSIFKSCVGLTLAELAEGFFQQALGVDLIKDDEIFFNDTDAPFEQRLEACLQATERARRETGQTVLYAINLTGP.VHRLPEKARRAARL..........ALLINVLPYGFDLLQRLAED..TVPLIAHPALAGALYP...DYGIAAPLLGTLMRLAGADLVL..............ALGLASRLTD.............PHRPTFPVPSAGIHPGLVPHMMDDF.GLDVVINAGGGIHGHPGGAAAGGRAFRAAIAAGVGGVPLEQAAAGSRDLRAALDQWG.................. [uniref90|D5MLU6 2,3-diketo-5-methylthiopentyl-1-phosphate enolase (DK-MTP-1-P enolase) n=1 Tax=NC10 bacterium 'Dutch sediment' RepID=D5MLU6_9BACT]
3FK4-A  : ......................GIIATYLIHDD.....EKKAEQIALGLTIG...........LKQHKGNVIHVEE............IIKIEYPLLNFSP.......DLPAILTTTFGKLSLD...GEVKLIDLTFSDELKKHFPGPKFGIDGIRNLLQVH....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENALTPLTKRIVSGKEVLQSVYETYGHKTLYAVNLTGR.TFDLKENAKRAVQA..........ILLFNVFAYGLDVLQSLAED..PVPIMAHPAVSGAYSA...LYGVSSPLLGKLLRYAGADFSL..............ALAISKYLTE...........DASFKKSFSVPSAGIHPGFVPFIVRDF.GKDVVINAGGGIHGHPNGAQGGGKAFRTAIDATLQNKPLHEV..DDINLHSALQIWG.................. [: RUBISCO-LIKE PROTEIN]
uniref90: ......................GIIATYLIHDD.....EKKAEQIALGLTIG...........LKQHKGNVLHVEE............IIKIEYPLLNFSP.......DLPAILTTTFGKLSLD...GEVKLIDLTFSDELKKHFPGPKFGIDGIRNLLQVH....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENALTPLTNRIVSGKEVLQSVYETYGHKTLYAVNVTGR.TFDLKENAKRAVQA..........ILLFNVFAYGLDVLQSLAED..PVPIMAHPAVSGAYSA...LYGISSPLLGKLLRYAGADFSL..............ALAISKYLTE...........DVFFKKSFSVPSAGIHPGFVPFIIRDF.GKDVVINAGGGIHGHPNGAQGGGKAFRTAIDATLQNKPLHEV..DDINLHSALQIWG.................. [uniref90|C3P745 2,3-diketo-5-methylthiopentyl-1-phosphate enolase n=71 Tax=Bacillus cereus group RepID=MTNW_BACAA]

NOTE: To save space, only 20 of 1110 template profile alignments are shown above. The complete set of alignments can be found in the file Homology_5hjx-~_profile.ali. The template profile contains structural alignments of 16 PDB files, which provide safe anchors for the remaining sequence-based alignments (only reliable regions shown).

In the alignment above, 451 of 470 target residues (96.0%) are aligned to template residues. Among these aligned residues, the sequence identity is 65.0% and the sequence similarity is 76.7% ('similar' means that the BLOSUM62 score is > 0). The following 4 loops had to be modeled (only the first of 2 similar loops in the homodimer is listed):

LoopN-terminal anchorLoop sequenceC-terminal anchor
1LETFAKYNSASHV
3KLIPAKGHGFLEV
5EIDETAFGDDPVKGGGLFKV
7WREKLGVHKNone

After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).

The resulting half-refined model has been saved as Homology_5hjx-~01_refined050.yob and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals0.120Optimal
Packing 1D-0.642Good
Packing 3D-1.139Satisfactory
Overall-0.763Good

Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as Homology_5hjx-~01_refined100.yob, the corresponding Z-scores are listed below:

Check typeQuality Z-scoreComment
Dihedrals0.421Optimal
Packing 1D-0.343Good
Packing 3D-1.299Satisfactory
Overall-0.677Good

Since the overall quality Z-score improved to -0.677 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.

NOTE: 8 residues contained in N- and C-terminal unaligned tails of the homodimeric model have been excluded from the Z-scores in both tables above, since they are not reliable (YASARA does not yet perform ab initio structure prediction) and would have mainly added noise to the result.

The final model for this template and alignment has been saved as Homology_5hjx-~01.yob, and is shown below, together with a plot of its overall quality Z-score, shown per residue:

6.13. Homology model 13/15, based on template 5HJX-~, alignment variant 02

This model is a homodimer, and based on the following profile-profile alignment:

(To improve readability, only up to ten lines of the complete target multiple sequence alignment (MSA) shown above are also displayed here (upside down). The template MSA has been shrunk and focused on structurally aligned PDB entries. The actual target-template alignment can be found in the middle at the line named 'Match'.)

Q08EW6  : .......................................................................................................................NNQGGGDIEHAKIHGIYMPERAIQLFDGPSKDISDMWRILGRPVKDGGYNAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEIQGNQVFSPMNQTIPLVVDAMKRAQDETGQAKLFSANITADDQYEMCARADFILEAFGP..DADKVAFLVDGYVGDPGMITTARSQYPNQYLHYHRAGHGAVNSPKIKRGYTAFVLAKMSRLQGASGAHVGTMGYGKME................................................................................................................................ [uniref90|Q08EW6 Ribulose 1,5-bisphosphate carboxylase/oxygenase large subunit (Fragment) n=1 Tax=uncultured marine bacterium RepID=Q08EW6_9BACT]
Q5DVV5  : ............................................................................................................................................................................IIKPKLGLRPKPFAEACYNFWLGGDFIKNDEPQGNQIWGPIKEVVPLVKDSLVRAQDDTGMAKLFSFNITADDHYEMLHRGEYILETFAEFSE..NIAFLVDGCVGGPGMVTTARRNFPDQFLHYHRAGHGAVTSDQSDRGYNMLVHMKMARLQGASGIHTGTMGYGKMEGAADDKVIAYMLERDSADGLSYHQEWEGMKATTPIICGGMNA...................................................................................... [uniref90|Q5DVV5 Ribulose-1,5-bisphosphate carboxylase oxygenase large subunit (Fragment) n=11 Tax=uncultured prokaryote RepID=Q5DVV5_9ZZZZ]
Q933G7  : ........................................................................................................................................VPPAYLRLFDGPSTTIKDLWRVLGRPVVDGGFIVGTIIKPKLGLRPQPFADACYDFWLGGDFIKNDEPQGNQVFAPFKDTVRAVNDAMRRAQDATGQPKLFSFNITADDHYEMLARGEYILETFGE..NADHVAFLVDGYVAGPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHVGTMGYGKMEGEASDRDSAFMITQDSAEGPYFKQEW...................................................................................................... [uniref90|Q933G7 Form II ribulose 1,5-bisphosphate carboxylase/oxygenase (Fragment) n=5 Tax=Rhodopseudomonas palustris RepID=Q933G7_RHOPA]
F2ZCE9  : .....................................................................................................................................DFYVPPDFLRLFDGPATTISNLWRVLGRPHQNGGFIVGTIVKPKLGLRPRPFADACYDFWLGGDFIKNDEPQGNQTFSPLKETIPLVADAMRRAQDETGEAKLFSANITADDHYEMVARGEFILDTFGEF..ADHVAFLVDGYVAGAAAVTTARRSFPQQYLHYHRAGHGAITSPQSKRGYTAFVHCKMARLQGASGIHTGTMSFGKMEGEAADRAIAFMLEQDSADGPYFHQEWHGMNPTTSIISG.......................................................................................... [uniref90|F2ZCE9 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=1 Tax=uncultured bacterium RepID=F2ZCE9_9BACT]
F2ZCD0  : ......................................................................................................................GNNQGMGDIANAQMQDFYVPPAMLALFDGPAKSINDLWTLLGRDNENGGYIAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEPQGNQVFCPLKKVLPLVHDAMKRAQDETGEAKLFSLNITADDHYEMCARADFGLETFGE..DAPRLAFLVDGFVGGPGMVTTARRQYSSQYLHYHRAGHGMITSPSSKRGYTAYILAKMSRLMGASGIHVGTMGYGKMEGGADDKIIAYMIERDECQGPFYYQKWHGMKPTTPIVSGGM........................................................................................ [uniref90|F2ZCD0 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=4 Tax=uncultured bacterium RepID=F2ZCD0_9BACT]
F5BZE6  : ......................................................................................................................GNNQGMGDVEYAKMIDFYMARSLLTLFDGPAMNITDMWRVLGRPQVNGGMVVGTIIKPKLGLRPKPFADACYMFWMGGDFIKNDEPQGNQVFAPTREIIPLVAEAMERAQQETGEAKIFSANITADDPFEMIRRGEFILEAFGK..NASHVAFLVDGYVGGPSAVTLCRRYFPNQFLHYHRAGHGAVTSNQSKRGYTVLTHMKMSRLQGASGIHTGTMGYGKMEGDKNEKMVAYMIERDEAMGVYYNQPWHGMTATTPIISGGMNALR.................................................................................... [uniref90|F5BZE6 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II (Fragment) n=1 Tax=alpha proteobacterium LM-5 RepID=F5BZE6_9PROT]
Q9FPW1  : LDQSSRYADLSLDEATLVKNGKHVLVAYIMKPKAGYDYLATAAHFAAESSTGTNVNVCTTDDFTKSVDALVYYIDPDSEE.........MKIAYPTLLFDRNIIDGRGMMCSFLTLAIGNNQGMGDVEYGKIYDFYLPPSFLRLYDGPAVNVEDMWRILGKGTSNGGLVDGTIIKPKLGLQPNPFGEACYSFWQGGDFIKNDEPQGNQVFCQMNECIPEVVKAMRACVKETGSSKLFSANITADDPEEMIARGKYIMSQFGPLSE..NCAFLVDGYVAGGTAVTCCRRNFPKQFLHYHRAGHGSVTSPQTQRGYTAFVHTKISRVIGASGIHVGTMSFGKMEGDASDKNIAYMLQDDEADGPYYRQEWQGMKETTPIISGGMNALRLPAFFENLGHSNVILTAGGGSFGHKDGPKIGAISCRQGEEAWKSLSDVIEYAKTHEEIKGAFLTFQKDADQIYPGWKEKLG... [uniref90|Q9FPW1 Ribulose 1,5-bisphosphate carboxylase oxygenase large subunit n=1 Tax=Symbiodinium sp. RepID=Q9FPW1_SYMSP]
E6VVI6  : .DQTSRYVNFDLKEDQLIADGNHVLCAYIYKPANGYGNVEVAAHFAAESSTGTNVEVCTTDDFTKGVDALVYEVSDASNGDS......LMKIAYPVELFDRNIIDGRAMLASFLTLCIGNNQGMGDVAYAKMHDFYVPRQYLELFDGPSKNIADFWRMLGRPTENGGMIAGTIVKPKLGLRPKPFADACYHFWLGGDFVKNDEPQGNQVFAPLKETITAVADAMRRAQDETGEAKIFSANITADDPREMIARGEFILNAFGE..NASRVAFLVDGYVAGPTAITTARRNFPNQFLHYHRAGHGAVTSPQAKRGYTAFVLSKMSRLQGASGIHTGTMGFGKMEGEMADKSMAYMIEREEAQGPYFKQKWYGMKATTPMISGGMNALRLPGFFDNLGHSNICQTSGGGAFGHLDGPTAGALSLRQSHDAWIQGVNLLDYAKEHNELARAFESFPGDADRFYPTWRHQL.... [uniref90|E6VVI6 Ribulose-bisphosphate carboxylase n=1 Tax=Desulfovibrio aespoeensis Aspo-2 RepID=E6VVI6_DESAO]
Q8RTI1  : MDQSNRYADLSLKEDDLIKGGNHVLVAYLMKPKTGYGYLEAAAHFSAESSTGTNVEVSTTDDFTKGVDALVYEIDEAK.........EIMKIAYPVDLFDRNITDGRAMIVSFLTLAIGNNQGMGDIAYAKMLDFYVPQKYLRLFDGPSKDISDLWRILGRPVVNGGYIAGTIIKPKLGLRPKPFAEAAYQFWLGGDFIKNDEPQGNQVFSPMRETIPLVYDSMKRAMDETGEAKLFSANITADDHYEMMARGEFILNTFGP..DADKVAFLVDGYVGGPGMVTTARRHFANQYLHYHRAGHGAVTSPSAKRGYTAFVLAKMSRLQGASGIHVGTMGYGKMEGDATDKNIAYMIERDSADGPFYHQEWYGMKPTTPIISGGMNALRLPGFFENLGHANLINTSGGGSYGHIDSPAAGAISLRQAYECWQQGADPIEFAKEHKEFARAFESFPGDADTIFPGWREKLGVHK [uniref90|Q8RTI1 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II n=1 Tax=magnetite-containing magnetic vibrio RepID=Q8RTI1_9PROT]
Q0F2Z8  : MDQSNRYADLSLNEADLIAGGKHLLVAYKLIPAKGYGFLEVAAHIAAESSTGTNVEVSTTDDFTRGVDALVYDIDETAFGDEGVTGGGLMKVAYPVELFDPNLIDGHYNVSHMWSLILGNNQGMGDHEGLRMLDFMVPECMIRKFDGPSAGIADLWKVLGRPEVDGGYISGTIIKPKLGLRPEPFAKACLDFWLGGDFIKNDEPQANQPFCPMKVVIPKVAEAMDRAQQETGQAKLFSANATADYHGECVARGEYILSEFAKYGNEKHVAFLIDGFVTGPAGVTTARRAFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLARLQGASGIHTGTMGYGKMEGHGKETVLAYMLERDECMGHYFNQKWYGMKPTAPIISGGMNALRLPGFFENLGHGNVINTCGGGSFGHIDSPAAGGKSLDQAYDCWKSGTDPIEYAKTHGEFARAFESFPGDADKLYPGWRDKLGVHK [uniref90|Q0F2Z8 Ribulose-bisphosphate carboxylase n=1 Tax=Mariprofundus ferrooxydans PV-1 RepID=Q0F2Z8_9PROT]
SecStr  : CCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCEEECCCCCCHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCEEEECCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEECCCCCCHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCHHCCCCCCCEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHHHHCCCC [Secondary structure predicted by PsiPred]
Target  : MDQSNRYANLNLKEEDLIKNGKHLLVAYKLIPAKGHGFLEVAAHVAAESSTGTNVEVSTTDDFTRGVDALVYEIDETAFGDDPVKGGGLFKVAYPVELFDPNLTDGTYNISHMWSLILGNNQGMGDHQGLRMLDFLVPEMMVRKFDGPSANISNLWKVLGRSETDGGYIAGTIIKPKLGLRPEPFAKACYDFWLGGDFIKNDEPQANQPFCPMEVVMPKVAEAMDRAQQATGQAKLFSANITADYYKEMIHRGDFVLETFAKYNSASHVAFLVDGFVTGPAGVTTARREFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLVRLMGASGMHTGTMGYGKMEGHGKETVLAYMLERDECQGPYFYQKWYGMKATTPIISGGMNALRLPGFFQNLGHGNVINTCGGGAFGHIDSPAAGGISLGQAYDCWKSGSDPIEYAKTHKEFARAFESFPKDGDKLFAGWREKLGVHK
Match   : MDQSNRYANLNLKE:|LI :G|H:L AY | P    :F||:AAH :AESSTGTNVEVSTTDDFTRGVDALVYE| | A         :L:K|AYP|ELFD N: DG   I: : :L |GNNQGMGD |  |M DF VP   :| FDGPS::I::LW|VLGR   :GG|I:GTIIKPKLGLRP|PFA:ACYDFWLGGDFI:NDEPQ:NQ F:P:: ::  VA|AM RAQ: TG|AKLFS NITAD | EM| RG|F|LETFA   :A:H|AFLVDG|V:GPA:VTTARR FP  |LH|HRAGHGAVTS :S  G   :   K|:RL:GASG:HTGTMG|GKMEG:: | :|AYM| :D ::GPYF|Q:W GM: TTPIISGGMNALR|PGFF:NLGH:N:I T:GGGAFGH|D: AAG: SL QA :CWK:G:DP|E|AK H|EFARAFESFP:D:DKL| :WR KL    
Template: MDQSNRYANLNLKESELIAGGRHVLCAYIMKPK...NFIQTAAHFVAESSTGTNVEVSTTDDFTRGVDALVYEV.DEAN........SLMKIAYPIELFDRNVIDGRAMIASFLTLTIGNNQGMGDVEYAKMYDFYVPPAYLKLFDGPSTTIKDLWRVLGRPVINGGFIVGTIIKPKLGLRPQPFANACYDFWLGGDFIXNDEPQGNQVFAPFKDTVRAVADAMRRAQDKTGEAKLFSFNITADDHYEMLARGEFILETFAD..NADHIAFLVDGYVAGPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHTGTMGFGKMEGEAADRAIAYMITEDAADGPYFHQEWLGMNPTTPIISGGMNALRMPGFFDNLGHSNLIMTAGGGAFGHVDGGAAGAKSLRQAEQCWKQGADPVEFAKDHREFARAFESFPQDADKLYPNWRAKL....
SecStr  : CCHHHHHCTTTTHHHHHHHHCCCEEEEEEEECC...HHHHHHHHHHHHCCCCCCCCTTTTHHHHHHCCCEEEEE.ETTT........EEEEEEETTTTCCCCCCCCCCCHHHHHHHHHGGGGCTTTTEEEEEEEEECHHHHHHCCCCCCCCHHHHHHHHHCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCEEEEETTTTCCTTTTHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCHHHHHHHHHHHHHHHHHC..TTTEEEEEEHHHHHCHHHHHHHHHHHCCCEEEEETTTTCCCCTTTTCCCCHHHHHHHHHHHHHCEEEEECTTTTCCCCCTTTTHHHHHHHHCEEEECCCEEEEETTTCCCEEEECCCCCCCHHHHHHHHHHCCCEEEEEHHHHHHCCCHHHHHHHHHHHHHHHHHHCCHHHHHHCCHHHHHHHHHHCHHHHHHHHCTTTTCC.... [Secondary structure assigned by YASARA]
1RSC-G  : ....LTYYTPDYTP.....KDTDLLAAFRFSPQ.....DEAGAAIAAESST..........TDMDRYKGKCYHI.EP...........FAFIAYPLDLFEE.......SVTNILTSIVGNVFGFKAIRSLRLEDIRFPVALVKTFQGPPHGIQVERDLLNKY....RPMLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKSQAETGEIKGHYLNVTAPTCEEMMKRAEFAKEL..........IIMHDFLTAGFTANTTLAKWCRGVLLHIHRAMHAVIDR...NHGIHFRVLAKCLRLSGGDHLH..............TLGFVDLMREDHIEA.FFTQDWASMPGVLPVASGGIHVWHMPALVEIF.GDDSVLQFGGGTLGHPWGNAPGATANRVALEACVQ...LREAGKWSPELAAALDLW................... [: RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (LARGE]
1GEH-B  : ..........GYEP.......RDIIAVFRVTPA.....EQAAGAVAAESST.GTWT..YEQERWADLSAKAYDF.HD...........IVRIAYPFHAFEE.......NLPGLLASIAGNIFGMKRVKGLRLEDLYFPEKLIREFDGPAFGIEGVRKMLEIK....RPIYGVVPKPKVGYSPEEFEKLAYDLLSNADYMKDDENLTSPWYNRFEERAEIMAKIIDKVENETGEKKTWFANITAD.LLEMEQRLEVLADL..........HAMVDVVITGWGALRYIRDLAAGLAIHGHRAMHAAFTR...YHGISMFVLAKLYRLIGIDQLH..............VIQNARILRESHYK...LEQKFYSIKAAFPTSSGGLHPGNIQPVIEAL.GTDIVLQLGGGTLGHPDGPAAGARAVRQAIDAIMQGIPLDEYAKTHKELARALEKW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE]
1SVD-A  : .....TYWMPEYTP.....LDSDILACFKITPQ.....EEAAAAVAAESSTG..........DMDYYKGRAYRI.ED...........YAFIAYPIDLFEE.......SVVNVFTSLVGNVFGFKAVRGLRLEDVRFPLAYVKTCGGPPHGIQVERDKMNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFMRWRDRFLFVQDATETAEAQTGERKGHYLNVTAPTPEEMYKRAEFAKEI..........IIMHDYITGGFTANTGLAKWCQGVLLHIHRAMHAVIDR...NHGIHFRVLTKILRLSGGDHLH..............TLGWIDLLRESFIP..FFDQDWGSMPGVFAVASGGIHVWHMPALVNIF.GDDSVLQFGGGTLGHPWGNAAGAAANRVALEACVE...LTAAAQHSPELKIAMETW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE]
2YBV-A  : ......YYTPDYTP.....KDTDILAAFRVTPQ.....EEAAAAVAAESSTG........LTDLDRYKGCCYDI.EP...........IAYIAYPLDLFEE.......SVTNMLTSIVGNVFGFKALKALRLEDLRIPVAYLKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKAQAETGEIKGHYLNVTAPTCEEMLKRAEFAKEL..........IIMHDFLTAGFTANTTLSKWCRGMLLHIHRAMHAVMDR...NHGIHFRVLAKCLRMSGGDHIH..............TLGFVDLLRENYIE..YFTQDWASMPGVMAVASGGIHVWHMPALVDIF.GDDAVLQFG.....HPWGNAPGATANRVALEACIQ...IREAARWSPELAAAC...................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN]
1BXN-C  : ....MGYWDGDYVP.....KDTDLLALFRITPQ.....VEAAAAVAGESST..WTV......ACDMYRAKAYRV.DP...........FCYVAYDLSLFEE.......SIANLTASIIGNVFSFKPIKAARLEDMRFPVAYVKTFAGPSTGIIVERERLDKF....RPLLGATTKPKLGLSGRNYGRVVYEGLKGLDFMKDDENINSQPFMHWRDRFLFVMDAVNKASAATGEVKGSYLNVTAGTMEEMYRRAEFAKSL..........IIMVD.LIVGWTCIQSMSNWCRDMILHLHRAGHGTYTR...NHGVSFRVIAKWLRLAGVDHMH..............VQGYYNVCRDAYTQ..FFDQDWASLRKVMPVASGGIHAGQMHQLIHLF.GDDVVLQFGGGTIGHPQGIQAGATANRVALEAMVL...LRDAARWCGPLRAALDTW................... [: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)]
1EJ7-L  : .....TYYTPEYQT.....KDTDILAAFRVTPQ.....EEAGAAVAAESSTGTWTTV.....SLDRYKGRCYRI.ER...........IAYVAYPLDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENVNSQPFMRWRDRFLFCAEALYKAQAETGEIKGHYLNATAGTCEEMIKRAVFAREL..........IVMHDYLTGGFTANTSLAHYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHIH..............TLGFVDLLRDDFVE..YFTQDWVSLPGVLPVASGGIHVWHMPALTEIF.GDDSVLQFGGGTLGHPWGNAPGAVANRVALEACVK...IREACKWSPELAAACEVW................... [: RUBISCO (LARGE SUBUNIT)]
1IWA-C  : ....MGYWNPDYQV.....KDTDVLALFRVTPQ.....IEAAAAVAGESST...........AADLYRAKAYKV.DQ...........FAYIAYELDLFEE.......SIANLTASIIGNVFGFKAVKALRLEDMRLPLAYLKTFQGPATGVILERERLDKF....RPLLGCTTKPKLGLSGKNYGRVVYEALKGLDFVKDDENINSQPFMRWRERYLFTMEAVNKASAATGEVKGHYLNVTAATMEEMYARANFAKEL..........IIMID.LVIGYTAIQTMAKWARDMILHLHRAGNSTYSR...NHGMNFRVICKWMRMAGVDHIH..............TRGFYKTLLLPKLE..FFDMEWASLRKVMPVASGGIHAGQMHQLIHYLG.EDVVLQFGGGTIGHPDGIQAGATANRVALEAMIL...LREAAKTCGALRTALDLW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE]
1TEL-B  : .....GFFAS...........QYLVLDYYLESV.....ETALAHFCSEQSTA........DEDFRVHAAKVIDY.EV...........RVTIAHPHCNFGP.......KIPNLLTAVCGETYFTPGVPVVKLMDIHFPDTYLADFEGPKFGIEGLRDILNAH....RPIFFGVVKPNIGLSPGEFAEIAYQSWLGLDIAKDDEMLADVTWSSIEERAAHLGKARRKAEAETGEPKIYLANITDE.VDSLMEKHDVAVRN..........ALLINALPVGLSAVRMLSNYT.QVPLIGHFPFIASFSR...KYGIHSKVMTKLQRLAGLDAVI..............VLENVIECTKP..........MGRIKPCLPVPGGSDSALTLQTVYEKVGNVDFGFVPGRGVFGHPMGPKAGAKSIRQAWEAIEQGISIETWAETHPELQAMVDQ.................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE, LARGE SUBUNIT]
2D69-A  : .....DFVDLNYEP.....GRDELIVEYYFEPN.....EEAAGRIASESSIGTW.........AKRSMAKVFYL.EK...........IAKIAYPLTLFEE.......SLVQLFSAVAGNVFGMKALKNLRLLDFHPPYEYLRHFKGPQFGVQGIREFMGVK....RPLTATVPKPKMGWSVEEYAEIAYELWSGIDLLKDDENFTSFPFNRFEERVRKLYRVRDRVEAETGETKEYLINITGP.VNIMEKRAEMVANE..........YVMIDIVVAGWSALQYMREVTEGLAIHAHRAMHAAFTR...RHGITMLALAKAARMIGVDQIH..............IKRINDFLLS...........WEHIRPVFPVASGGLHPGLMPELIRLF.GKDLVIQAGGGVMGHPDGPRAGAKALRDAIDAAIEGVDLDEKAKSSPELKKSLREV................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE]
2QYG-D  : .....GFYAK...........NYIELDFDFECA.....HEAAAHLCSEQSTA...........RPRFAAKVLEL.SA...........RVTIAHPHGNF........AKIPNLLSAVCGEVFFSPGIPLIRLQDIRFPEPYLAAFDGPRFGIAGVRERLQAF....RPIFFGVIKPNIGLPPQPFAELGYQSWTGLDIAKDDEMLADVDWCPLAERAALLGDACRRASAETGVPKIYLANITDE.VDRLTELHDVAVAN..........ALLINAMPVGLSAVRMLRKHA.TVPLIAHFPFIAAFSR...NYGIHSRVMTRLQRLAGFDVVI..............VLDCIRACLE...........MGPIKPCLPVPGGSDSAATLENVYRKVGSADFGFVPGRGVFGHPMGPAAGATSIRQAWDAIAAGIPVPDHAASHPELAAALRAF................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE-LIKE PROTEIN 2]
2V67-A  : ....LTYYTPDYVV......DTDILAAFRMTPQ.....EECGAAVAAESST...........SLDRYKGRCYDI.EP...........IAYVAYXIDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFVGXPHGIQVERDKLNKY....RGLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTXDDENVNSQPFMRWRDRFLFVAEAIYKAQAETGEVKGHYLNATAGTCEEMMKRAVXAKEL..........IIMHDYLTGGFTANTSLAIYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHLH..............ILGFVDLMRDDYVE..YFTQDWXSMPGVMPVASGGIHVWHMPALVEIF.GDDACLQFGGGTLGHPWGNAPGAAANRVALEACTQ...IRSACKWSPELAAACEVW................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN]
3NWR-A  : ....................EDTLEADYLIET......ARVADVMAGEQSSG............ARSRASVLRI.EE...........RITLSFPLANI.........NLPTLAATVAGNLYDLGEVTGVRLLSLRLPASYRARFELPRHGVAGTRALTDVK....RPMIGTIIKPNVGLSAAETAALVRELCEAVDFIXDDEVCANPAHAPLAERVRAVMSEVRRYRERSGRPVMVAFNITDD.LDAMRRHAELVERE..........CVMASINWCGFSAIQSLRRTT.PLVLHAHRNGYGMMSR...ALGMSFQAYQTLWRLSGVDHMH..............VIESARDCATP...............AVLPAFSSGQWAGTVQATFDAVRSTDLLFMSGGGILAHPDGPAAGVTSVRQAWAAVQAGTPLPVYAEHMPELRRALAFF................... [: A RUBISCO-LIKE PROTEIN]
3QFW-B  : ......................RIVATYHIAS......EQRALALAIEQSVEC............NIVGRVEDV.AE...........AVRIGLAAATAP.......AEPGQLLNMLFGNSSIQPD...IALADVELPAHYLTAFGGPRVGLAGIRTLTGAQ....RALTASALKP.QGLSPAALASIAHQLALGVDLIKDDHGLADQAFSPFAERAAAVGKAVREANAARGGRTLYAPNISG.TLDDMRRQLGVIRDE..........AVLVAPMIVGVSNFHAIVKEAAGLVVVAHPAMAGAA........IAAPLLGRLFRLFGADATV..............CLALAQAARD...........FGKLNACIPTPAGGIMLQRVNELLRFYG.QDVMLLI..........LTEQASRFVNKVADYGQR....................................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE]
uniref90: ......................RIIVTYQVAA......AARAEALAIEQSVEC............EIVGRVEAI.AP...........SVRVSLASATAP.......AEPGQLLNMLFGNSSIQPD...VTLADVELPPAYPAAFGGPKLGISGLRAKLGAP....RALTGSALKP.QGLAPEALAGLAHRLALGVDLIKDDHGIADQAFSPFAARVPAVARAMREACAVRGAAMLYAPHVSG.SLDDMRRQLDIVRRE..........VVMLMPMIVGLANFHLIAKEAEGLIVLAHPSLAGAQ........IAPDLLGKLFRLLGADATI..............CRALADAARR...........WHDLKPCLPVPAGGIAIDRIKELLAFYG.TDVMLLI..........LTEHAARFTAEVASHGQ........................................ [uniref90|Q6N7T7 Ribulose bisphosphate carboxylase-like protein 1 n=2 Tax=Rhodopseudomonas palustris RepID=RBLL1_RHOPA]
2ZVI-A  : ......................ELLATYLLT.......EKKAEQIATGLTVG...........MQKHKGRVIKV.EE...........VITIAYPEINFSQ.......DIPALLTTVFGKLSL...DGKIKLIDLHFSEAFKRALPGPKFGVYGIRKLLGE.....RPLLMSIFKGVIGRDLSDIKEQLRQQALGVDLIKDDEIFFETGLAPFETRIAEGKQILKETYEQTGHKTLYAVNLTGR.TADLKDKARRAAEL..........ALLFNVFAYGLDVMQGLAED..PVPIMAHPAVSGAFTS...FYGFSHALLGKLNRYCGADFSL..............ALAIHEECVR.............AFNQTFAVPSAGIHPGMVPLLMRDF.GIDHIINAGGGVHGHPNGAQGGGRAFRAIIDAVLEAQPIDEKAEQCKDLKLALDKWGK................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE]
uniref90: ......................................HKQAKIIAVGQTAG...........LRQHLAEVIEI.KT.............KIRFPEINVEN.......DLASLLTMIFGKYSM...AGAAKVIGVHLPESYGQR...PKFGITGIRKILNV.....RPLIMAIFKPALGLSAADHAVILKQVADALDIIKDDEILGDLETAPTLKRLEACRQVLEAIKQQTGRTVLYAVNVTGK.ADKLIEKARLLVKE..........ALLLNVLTYGFSVLEALAAD..NVPIFAHPAFAGAMCA...DTGLSYSVIGRFMAHGGVDAVL..............EKKIRDSLRS.............VF....PVPSAGIHPGIVPKAIADY.GDDVILNAGTGIMDHPNNPGAGVKAFFEALERVKTGQSFTLDTVPEGALKQALQKWG.................. [uniref90|B7KIK8 Ribulose-bisphosphate carboxylase n=1 Tax=Cyanothece sp. PCC 7424 RepID=B7KIK8_CYAP7]
2OEK-B  : ......................AVMATYLLHDE.....RKKAEGIALGLTIG...........LRKHKGEVVAI.EE...........IVKIAYPTVNFSA.......DLPALLVTTFGKLSLD...GEVRLLDLEFPDEWKRQFPGPRFGIDGIRDRVGVH....RPLLMSIFKGMIGRDLAYLTSELKKQALGVDLVXDDEILFDSELLPFEKRITEGKAALQEVYEQTGKRTLYAVNLTGK.TFALKDKAKRAAEL..........VLLFNVFAYGLDVLQALRED..AVPIMAHPAFSGAVTP...FYGVAPSLWGKLLRLAGADFVL..............ALGIARALTD.............PFARAFPVPSAGIHPGLVPLIIRDF.GLDTIVNAGGGIHGHPDGAIGGGRAFRAAIDAVLAGRPLRAAAAENEALQKAIDRWGV................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE ENOLASE]
uniref90: .......................VIATYRLAGG.....TKKAETIALGMTVG...........LQRHAGRVVSV.DA...........LIRIAYPLANLTP.......DLPSLLTATFGKLSMD...GKIRLLDLTLPPTFAAAFPGPKLGVEGIRERLGVH....RPLLMSIFKSCVGLTLAELAEGFFQQALGVDLIKDDEIFFNDTDAPFEQRLEACLQATERARRETGQTVLYAINLTGP.VHRLPEKARRAARL..........ALLINVLPYGFDLLQRLAED..TVPLIAHPALAGALYP...DYGIAAPLLGTLMRLAGADLVL..............ALGLASRLTD.............PHRPTFPVPSAGIHPGLVPHMMDDF.GLDVVINAGGGIHGHPGGAAAGGRAFRAAIAAGVGGVPLEQAAAGSRDLRAALDQWG.................. [uniref90|D5MLU6 2,3-diketo-5-methylthiopentyl-1-phosphate enolase (DK-MTP-1-P enolase) n=1 Tax=NC10 bacterium 'Dutch sediment' RepID=D5MLU6_9BACT]
3FK4-A  : ......................GIIATYLIHDD.....EKKAEQIALGLTIG...........LKQHKGNVIHV.EE...........IIKIEYPLLNFSP.......DLPAILTTTFGKLSLD...GEVKLIDLTFSDELKKHFPGPKFGIDGIRNLLQVH....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENALTPLTKRIVSGKEVLQSVYETYGHKTLYAVNLTGR.TFDLKENAKRAVQA..........ILLFNVFAYGLDVLQSLAED..PVPIMAHPAVSGAYSA...LYGVSSPLLGKLLRYAGADFSL..............ALAISKYLTE...........DASFKKSFSVPSAGIHPGFVPFIVRDF.GKDVVINAGGGIHGHPNGAQGGGKAFRTAIDATLQNKPLHEV..DDINLHSALQIWG.................. [: RUBISCO-LIKE PROTEIN]
uniref90: ......................GIIATYLIHDD.....EKKAEQIALGLTIG...........LKQHKGNVLHV.EE...........IIKIEYPLLNFSP.......DLPAILTTTFGKLSLD...GEVKLIDLTFSDELKKHFPGPKFGIDGIRNLLQVH....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENALTPLTNRIVSGKEVLQSVYETYGHKTLYAVNVTGR.TFDLKENAKRAVQA..........ILLFNVFAYGLDVLQSLAED..PVPIMAHPAVSGAYSA...LYGISSPLLGKLLRYAGADFSL..............ALAISKYLTE...........DVFFKKSFSVPSAGIHPGFVPFIIRDF.GKDVVINAGGGIHGHPNGAQGGGKAFRTAIDATLQNKPLHEV..DDINLHSALQIWG.................. [uniref90|C3P745 2,3-diketo-5-methylthiopentyl-1-phosphate enolase n=71 Tax=Bacillus cereus group RepID=MTNW_BACAA]

NOTE: To save space, only 20 of 1110 template profile alignments are shown above. The complete set of alignments can be found in the file Homology_5hjx-~_profile.ali. The template profile contains structural alignments of 16 PDB files, which provide safe anchors for the remaining sequence-based alignments (only reliable regions shown).

In the alignment above, 452 of 470 target residues (96.2%) are aligned to template residues. Among these aligned residues, the sequence identity is 64.6% and the sequence similarity is 76.5% ('similar' means that the BLOSUM62 score is > 0). The following 5 loops had to be modeled (only the first of 2 similar loops in the homodimer is listed):

LoopN-terminal anchorLoop sequenceC-terminal anchor
1LVYEIDETAFGDD
3LETFAKYNSASHV
5KLIPAKGHGFLEV
7DETAFGDDPVKGGGLFKV
9WREKLGVHKNone

After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).

The resulting half-refined model has been saved as Homology_5hjx-~02_refined050.yob and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals0.258Optimal
Packing 1D-0.547Good
Packing 3D-1.090Satisfactory
Overall-0.683Good

Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as Homology_5hjx-~02_refined100.yob, the corresponding Z-scores are listed below:

Check typeQuality Z-scoreComment
Dihedrals0.433Optimal
Packing 1D-0.192Good
Packing 3D-1.330Satisfactory
Overall-0.630Good

Since the overall quality Z-score improved to -0.630 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.

NOTE: 8 residues contained in N- and C-terminal unaligned tails of the homodimeric model have been excluded from the Z-scores in both tables above, since they are not reliable (YASARA does not yet perform ab initio structure prediction) and would have mainly added noise to the result.

The final model for this template and alignment has been saved as Homology_5hjx-~02.yob, and is shown below, together with a plot of its overall quality Z-score, shown per residue:

6.14. Homology model 14/15, based on template 5HJX-~, alignment variant 03

This model is a homodimer, and based on the following profile-profile alignment:

(To improve readability, only up to ten lines of the complete target multiple sequence alignment (MSA) shown above are also displayed here (upside down). The template MSA has been shrunk and focused on structurally aligned PDB entries. The actual target-template alignment can be found in the middle at the line named 'Match'.)

Q08EW6  : .......................................................................................................................NNQGGGDIEHAKIHGIYMPERAIQLFDGPSKDISDMWRILGRPVKDGGYNAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEIQGNQVFSPMNQTIPLVVDAMKRAQDETGQAKLFSANITADDQYEMCARADFILEAFGP..DADKVAFLVDGYVGDPGMITTARSQYPNQYLHYHRAGHGAVNSPKIKRGYTAFVLAKMSRLQGASGAHVGTMGYGKME................................................................................................................................ [uniref90|Q08EW6 Ribulose 1,5-bisphosphate carboxylase/oxygenase large subunit (Fragment) n=1 Tax=uncultured marine bacterium RepID=Q08EW6_9BACT]
Q5DVV5  : ............................................................................................................................................................................IIKPKLGLRPKPFAEACYNFWLGGDFIKNDEPQGNQIWGPIKEVVPLVKDSLVRAQDDTGMAKLFSFNITADDHYEMLHRGEYILETFAEFSE..NIAFLVDGCVGGPGMVTTARRNFPDQFLHYHRAGHGAVTSDQSDRGYNMLVHMKMARLQGASGIHTGTMGYGKMEGAADDKVIAYMLERDSADGLSYHQEWEGMKATTPIICGGMNA...................................................................................... [uniref90|Q5DVV5 Ribulose-1,5-bisphosphate carboxylase oxygenase large subunit (Fragment) n=11 Tax=uncultured prokaryote RepID=Q5DVV5_9ZZZZ]
Q933G7  : ........................................................................................................................................VPPAYLRLFDGPSTTIKDLWRVLGRPVVDGGFIVGTIIKPKLGLRPQPFADACYDFWLGGDFIKNDEPQGNQVFAPFKDTVRAVNDAMRRAQDATGQPKLFSFNITADDHYEMLARGEYILETFGE..NADHVAFLVDGYVAGPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHVGTMGYGKMEGEASDRDSAFMITQDSAEGPYFKQEW...................................................................................................... [uniref90|Q933G7 Form II ribulose 1,5-bisphosphate carboxylase/oxygenase (Fragment) n=5 Tax=Rhodopseudomonas palustris RepID=Q933G7_RHOPA]
F2ZCE9  : .....................................................................................................................................DFYVPPDFLRLFDGPATTISNLWRVLGRPHQNGGFIVGTIVKPKLGLRPRPFADACYDFWLGGDFIKNDEPQGNQTFSPLKETIPLVADAMRRAQDETGEAKLFSANITADDHYEMVARGEFILDTFGEF..ADHVAFLVDGYVAGAAAVTTARRSFPQQYLHYHRAGHGAITSPQSKRGYTAFVHCKMARLQGASGIHTGTMSFGKMEGEAADRAIAFMLEQDSADGPYFHQEWHGMNPTTSIISG.......................................................................................... [uniref90|F2ZCE9 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=1 Tax=uncultured bacterium RepID=F2ZCE9_9BACT]
F2ZCD0  : ......................................................................................................................GNNQGMGDIANAQMQDFYVPPAMLALFDGPAKSINDLWTLLGRDNENGGYIAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEPQGNQVFCPLKKVLPLVHDAMKRAQDETGEAKLFSLNITADDHYEMCARADFGLETFGE..DAPRLAFLVDGFVGGPGMVTTARRQYSSQYLHYHRAGHGMITSPSSKRGYTAYILAKMSRLMGASGIHVGTMGYGKMEGGADDKIIAYMIERDECQGPFYYQKWHGMKPTTPIVSGGM........................................................................................ [uniref90|F2ZCD0 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=4 Tax=uncultured bacterium RepID=F2ZCD0_9BACT]
F5BZE6  : ......................................................................................................................GNNQGMGDVEYAKMIDFYMARSLLTLFDGPAMNITDMWRVLGRPQVNGGMVVGTIIKPKLGLRPKPFADACYMFWMGGDFIKNDEPQGNQVFAPTREIIPLVAEAMERAQQETGEAKIFSANITADDPFEMIRRGEFILEAFGK..NASHVAFLVDGYVGGPSAVTLCRRYFPNQFLHYHRAGHGAVTSNQSKRGYTVLTHMKMSRLQGASGIHTGTMGYGKMEGDKNEKMVAYMIERDEAMGVYYNQPWHGMTATTPIISGGMNALR.................................................................................... [uniref90|F5BZE6 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II (Fragment) n=1 Tax=alpha proteobacterium LM-5 RepID=F5BZE6_9PROT]
Q9FPW1  : LDQSSRYADLSLDEATLVKNGKHVLVAYIMKPKAGYDYLATAAHFAAESSTGTNVNVCTTDDFTKSVDALVYYIDPDSEE.........MKIAYPTLLFDRNIIDGRGMMCSFLTLAIGNNQGMGDVEYGKIYDFYLPPSFLRLYDGPAVNVEDMWRILGKGTSNGGLVDGTIIKPKLGLQPNPFGEACYSFWQGGDFIKNDEPQGNQVFCQMNECIPEVVKAMRACVKETGSSKLFSANITADDPEEMIARGKYIMSQFGPLSE..NCAFLVDGYVAGGTAVTCCRRNFPKQFLHYHRAGHGSVTSPQTQRGYTAFVHTKISRVIGASGIHVGTMSFGKMEGDASDKNIAYMLQDDEADGPYYRQEWQGMKETTPIISGGMNALRLPAFFENLGHSNVILTAGGGSFGHKDGPKIGAISCRQGEEAWKSLSDVIEYAKTHEEIKGAFLTFQKDADQIYPGWKEKLG... [uniref90|Q9FPW1 Ribulose 1,5-bisphosphate carboxylase oxygenase large subunit n=1 Tax=Symbiodinium sp. RepID=Q9FPW1_SYMSP]
E6VVI6  : .DQTSRYVNFDLKEDQLIADGNHVLCAYIYKPANGYGNVEVAAHFAAESSTGTNVEVCTTDDFTKGVDALVYEVSDASNGDS......LMKIAYPVELFDRNIIDGRAMLASFLTLCIGNNQGMGDVAYAKMHDFYVPRQYLELFDGPSKNIADFWRMLGRPTENGGMIAGTIVKPKLGLRPKPFADACYHFWLGGDFVKNDEPQGNQVFAPLKETITAVADAMRRAQDETGEAKIFSANITADDPREMIARGEFILNAFGE..NASRVAFLVDGYVAGPTAITTARRNFPNQFLHYHRAGHGAVTSPQAKRGYTAFVLSKMSRLQGASGIHTGTMGFGKMEGEMADKSMAYMIEREEAQGPYFKQKWYGMKATTPMISGGMNALRLPGFFDNLGHSNICQTSGGGAFGHLDGPTAGALSLRQSHDAWIQGVNLLDYAKEHNELARAFESFPGDADRFYPTWRHQL.... [uniref90|E6VVI6 Ribulose-bisphosphate carboxylase n=1 Tax=Desulfovibrio aespoeensis Aspo-2 RepID=E6VVI6_DESAO]
Q8RTI1  : MDQSNRYADLSLKEDDLIKGGNHVLVAYLMKPKTGYGYLEAAAHFSAESSTGTNVEVSTTDDFTKGVDALVYEIDEAK.........EIMKIAYPVDLFDRNITDGRAMIVSFLTLAIGNNQGMGDIAYAKMLDFYVPQKYLRLFDGPSKDISDLWRILGRPVVNGGYIAGTIIKPKLGLRPKPFAEAAYQFWLGGDFIKNDEPQGNQVFSPMRETIPLVYDSMKRAMDETGEAKLFSANITADDHYEMMARGEFILNTFGP..DADKVAFLVDGYVGGPGMVTTARRHFANQYLHYHRAGHGAVTSPSAKRGYTAFVLAKMSRLQGASGIHVGTMGYGKMEGDATDKNIAYMIERDSADGPFYHQEWYGMKPTTPIISGGMNALRLPGFFENLGHANLINTSGGGSYGHIDSPAAGAISLRQAYECWQQGADPIEFAKEHKEFARAFESFPGDADTIFPGWREKLGVHK [uniref90|Q8RTI1 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II n=1 Tax=magnetite-containing magnetic vibrio RepID=Q8RTI1_9PROT]
Q0F2Z8  : MDQSNRYADLSLNEADLIAGGKHLLVAYKLIPAKGYGFLEVAAHIAAESSTGTNVEVSTTDDFTRGVDALVYDIDETAFGDEGVTGGGLMKVAYPVELFDPNLIDGHYNVSHMWSLILGNNQGMGDHEGLRMLDFMVPECMIRKFDGPSAGIADLWKVLGRPEVDGGYISGTIIKPKLGLRPEPFAKACLDFWLGGDFIKNDEPQANQPFCPMKVVIPKVAEAMDRAQQETGQAKLFSANATADYHGECVARGEYILSEFAKYGNEKHVAFLIDGFVTGPAGVTTARRAFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLARLQGASGIHTGTMGYGKMEGHGKETVLAYMLERDECMGHYFNQKWYGMKPTAPIISGGMNALRLPGFFENLGHGNVINTCGGGSFGHIDSPAAGGKSLDQAYDCWKSGTDPIEYAKTHGEFARAFESFPGDADKLYPGWRDKLGVHK [uniref90|Q0F2Z8 Ribulose-bisphosphate carboxylase n=1 Tax=Mariprofundus ferrooxydans PV-1 RepID=Q0F2Z8_9PROT]
SecStr  : CCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCEEECCCCCCHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCEEEECCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEECCCCCCHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCHHCCCCCCCEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHHHHCCCC [Secondary structure predicted by PsiPred]
Target  : MDQSNRYANLNLKEEDLIKNGKHLLVAYKLIPAKGHGFLEVAAHVAAESSTGTNVEVSTTDDFTRGVDALVYEIDETAFGDDPVKGGGLFKVAYPVELFDPNLTDGTYNISHMWSLILGNNQGMGDHQGLRMLDFLVPEMMVRKFDGPSANISNLWKVLGRSETDGGYIAGTIIKPKLGLRPEPFAKACYDFWLGGDFIKNDEPQANQPFCPMEVVMPKVAEAMDRAQQATGQAKLFSANITADYYKEMIHRGDFVLETFAKYNSASHVAFLVDGFVTGPAGVTTARREFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLVRLMGASGMHTGTMGYGKMEGHGKETVLAYMLERDECQGPYFYQKWYGMKATTPIISGGMNALRLPGFFQNLGHGNVINTCGGGAFGHIDSPAAGGISLGQAYDCWKSGSDPIEYAKTHKEFARAFESFPKDGDKLFAGWREKLGVHK
Match   : MDQSNRYANLNLKE:|LI :G|H:L AY | P    :F||:AAH :AESSTGTNVEVSTTDDFTRGVDALVYE|DE:          :L:K|AYP|ELFD N: DG   I: : :L |GNNQGMGD |  |M DF VP   :| FDGPS::I::LW|VLGR   :GG|I:GTIIKPKLGLRP|PFA:ACYDFWLGGDFI:NDEPQ:NQ F:P:: ::  VA|AM RAQ: TG|AKLFS NITAD | EM| RG|F|LETFA     :H|AFLVD   ::PA:VTTARR FP  |LH|HRAGHGAVTS :S  G   :   K|:RL:GASG:HTGTMG|GKMEG:: | :|AYM| :D ::GPYF|Q:W GM: TTPIISGGMNALR|PGFF:NLGH:N:I T:GGGAFGH|D: AAG: SL QA :CWK:G:DP|E|AK H|EFARAFESFP:D:DKL| :WR KL    
Template: MDQSNRYANLNLKESELIAGGRHVLCAYIMKPK...NFIQTAAHFVAESSTGTNVEVSTTDDFTRGVDALVYEVDEA..........SLMKIAYPIELFDRNVIDGRAMIASFLTLTIGNNQGMGDVEYAKMYDFYVPPAYLKLFDGPSTTIKDLWRVLGRPVINGGFIVGTIIKPKLGLRPQPFANACYDFWLGGDFIXNDEPQGNQVFAPFKDTVRAVADAMRRAQDKTGEAKLFSFNITADDHYEMLARGEFILETFAD....DHIAFLVD.GYVAPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHTGTMGFGKMEGEAADRAIAYMITEDAADGPYFHQEWLGMNPTTPIISGGMNALRMPGFFDNLGHSNLIMTAGGGAFGHVDGGAAGAKSLRQAEQCWKQGADPVEFAKDHREFARAFESFPQDADKLYPNWRAKL....
SecStr  : CCHHHHHCTTTTHHHHHHHHCCCEEEEEEEECC...HHHHHHHHHHHHCCCCCCCCTTTTHHHHHHCCCEEEEEETT..........EEEEEEETTTTCCCCCCCCCCCHHHHHHHHHGGGGCTTTTEEEEEEEEECHHHHHHCCCCCCCCHHHHHHHHHCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCEEEEETTTTCCTTTTHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCHHHHHHHHHHHHHHHHHC....TEEEEEEH.HHHHHHHHHHHHHHHCCCEEEEETTTTCCCCTTTTCCCCHHHHHHHHHHHHHCEEEEECTTTTCCCCCTTTTHHHHHHHHCEEEECCCEEEEETTTCCCEEEECCCCCCCHHHHHHHHHHCCCEEEEEHHHHHHCCCHHHHHHHHHHHHHHHHHHCCHHHHHHCCHHHHHHHHHHCHHHHHHHHCTTTTCC.... [Secondary structure assigned by YASARA]
1RSC-G  : ....LTYYTPDYTP.....KDTDLLAAFRFSPQ.....DEAGAAIAAESST..........TDMDRYKGKCYHIEP............FAFIAYPLDLFEE.......SVTNILTSIVGNVFGFKAIRSLRLEDIRFPVALVKTFQGPPHGIQVERDLLNKY....RPMLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKSQAETGEIKGHYLNVTAPTCEEMMKRAEFAKEL..........IIMHD.FLTAFTANTTLAKWCRGVLLHIHRAMHAVIDR...NHGIHFRVLAKCLRLSGGDHLH..............TLGFVDLMREDHIEA.FFTQDWASMPGVLPVASGGIHVWHMPALVEIF.GDDSVLQFGGGTLGHPWGNAPGATANRVALEACVQ...LREAGKWSPELAAALDLW................... [: RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (LARGE]
1GEH-B  : ..........GYEP.......RDIIAVFRVTPA.....EQAAGAVAAESST.GTWT..YEQERWADLSAKAYDFHD............IVRIAYPFHAFEE.......NLPGLLASIAGNIFGMKRVKGLRLEDLYFPEKLIREFDGPAFGIEGVRKMLEIK....RPIYGVVPKPKVGYSPEEFEKLAYDLLSNADYMKDDENLTSPWYNRFEERAEIMAKIIDKVENETGEKKTWFANITAD.LLEMEQRLEVLADL..........HAMVD.VVITWGALRYIRDLAAGLAIHGHRAMHAAFTR...YHGISMFVLAKLYRLIGIDQLH..............VIQNARILRESHYK...LEQKFYSIKAAFPTSSGGLHPGNIQPVIEAL.GTDIVLQLGGGTLGHPDGPAAGARAVRQAIDAIMQGIPLDEYAKTHKELARALEKW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE]
1SVD-A  : .....TYWMPEYTP.....LDSDILACFKITPQ.....EEAAAAVAAESSTG..........DMDYYKGRAYRIED............YAFIAYPIDLFEE.......SVVNVFTSLVGNVFGFKAVRGLRLEDVRFPLAYVKTCGGPPHGIQVERDKMNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFMRWRDRFLFVQDATETAEAQTGERKGHYLNVTAPTPEEMYKRAEFAKEI..........IIMHD.YITGFTANTGLAKWCQGVLLHIHRAMHAVIDR...NHGIHFRVLTKILRLSGGDHLH..............TLGWIDLLRESFIP..FFDQDWGSMPGVFAVASGGIHVWHMPALVNIF.GDDSVLQFGGGTLGHPWGNAAGAAANRVALEACVE...LTAAAQHSPELKIAMETW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE]
2YBV-A  : ......YYTPDYTP.....KDTDILAAFRVTPQ.....EEAAAAVAAESSTG........LTDLDRYKGCCYDIEP............IAYIAYPLDLFEE.......SVTNMLTSIVGNVFGFKALKALRLEDLRIPVAYLKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKAQAETGEIKGHYLNVTAPTCEEMLKRAEFAKEL..........IIMHD.FLTAFTANTTLSKWCRGMLLHIHRAMHAVMDR...NHGIHFRVLAKCLRMSGGDHIH..............TLGFVDLLRENYIE..YFTQDWASMPGVMAVASGGIHVWHMPALVDIF.GDDAVLQFG.....HPWGNAPGATANRVALEACIQ...IREAARWSPELAAAC...................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN]
1BXN-C  : ....MGYWDGDYVP.....KDTDLLALFRITPQ.....VEAAAAVAGESST..WTV......ACDMYRAKAYRVDP............FCYVAYDLSLFEE.......SIANLTASIIGNVFSFKPIKAARLEDMRFPVAYVKTFAGPSTGIIVERERLDKF....RPLLGATTKPKLGLSGRNYGRVVYEGLKGLDFMKDDENINSQPFMHWRDRFLFVMDAVNKASAATGEVKGSYLNVTAGTMEEMYRRAEFAKSL..........IIMVD..LIVWTCIQSMSNWCRDMILHLHRAGHGTYTR...NHGVSFRVIAKWLRLAGVDHMH..............VQGYYNVCRDAYTQ..FFDQDWASLRKVMPVASGGIHAGQMHQLIHLF.GDDVVLQFGGGTIGHPQGIQAGATANRVALEAMVL...LRDAARWCGPLRAALDTW................... [: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)]
1EJ7-L  : .....TYYTPEYQT.....KDTDILAAFRVTPQ.....EEAGAAVAAESSTGTWTTV.....SLDRYKGRCYRIER............IAYVAYPLDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENVNSQPFMRWRDRFLFCAEALYKAQAETGEIKGHYLNATAGTCEEMIKRAVFAREL..........IVMHD.YLTGFTANTSLAHYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHIH..............TLGFVDLLRDDFVE..YFTQDWVSLPGVLPVASGGIHVWHMPALTEIF.GDDSVLQFGGGTLGHPWGNAPGAVANRVALEACVK...IREACKWSPELAAACEVW................... [: RUBISCO (LARGE SUBUNIT)]
1IWA-C  : ....MGYWNPDYQV.....KDTDVLALFRVTPQ.....IEAAAAVAGESST...........AADLYRAKAYKVDQ............FAYIAYELDLFEE.......SIANLTASIIGNVFGFKAVKALRLEDMRLPLAYLKTFQGPATGVILERERLDKF....RPLLGCTTKPKLGLSGKNYGRVVYEALKGLDFVKDDENINSQPFMRWRERYLFTMEAVNKASAATGEVKGHYLNVTAATMEEMYARANFAKEL..........IIMID..LVIYTAIQTMAKWARDMILHLHRAGNSTYSR...NHGMNFRVICKWMRMAGVDHIH..............TRGFYKTLLLPKLE..FFDMEWASLRKVMPVASGGIHAGQMHQLIHYLG.EDVVLQFGGGTIGHPDGIQAGATANRVALEAMIL...LREAAKTCGALRTALDLW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE]
1TEL-B  : .....GFFAS...........QYLVLDYYLESV.....ETALAHFCSEQSTA........DEDFRVHAAKVIDYEV............RVTIAHPHCNFGP.......KIPNLLTAVCGETYFTPGVPVVKLMDIHFPDTYLADFEGPKFGIEGLRDILNAH....RPIFFGVVKPNIGLSPGEFAEIAYQSWLGLDIAKDDEMLADVTWSSIEERAAHLGKARRKAEAETGEPKIYLANITDE.VDSLMEKHDVAVRN..........ALLIN.ALPVLSAVRMLSNYT.QVPLIGHFPFIASFSR...KYGIHSKVMTKLQRLAGLDAVI..............VLENVIECTKP..........MGRIKPCLPVPGGSDSALTLQTVYEKVGNVDFGFVPGRGVFGHPMGPKAGAKSIRQAWEAIEQGISIETWAETHPELQAMVDQ.................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE, LARGE SUBUNIT]
2D69-A  : .....DFVDLNYEP.....GRDELIVEYYFEPN.....EEAAGRIASESSIGTW.........AKRSMAKVFYLEK............IAKIAYPLTLFEE.......SLVQLFSAVAGNVFGMKALKNLRLLDFHPPYEYLRHFKGPQFGVQGIREFMGVK....RPLTATVPKPKMGWSVEEYAEIAYELWSGIDLLKDDENFTSFPFNRFEERVRKLYRVRDRVEAETGETKEYLINITGP.VNIMEKRAEMVANE..........YVMID.IVVAWSALQYMREVTEGLAIHAHRAMHAAFTR...RHGITMLALAKAARMIGVDQIH..............IKRINDFLLS...........WEHIRPVFPVASGGLHPGLMPELIRLF.GKDLVIQAGGGVMGHPDGPRAGAKALRDAIDAAIEGVDLDEKAKSSPELKKSLREV................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE]
2QYG-D  : .....GFYAK...........NYIELDFDFECA.....HEAAAHLCSEQSTA...........RPRFAAKVLELSA............RVTIAHPHGNF........AKIPNLLSAVCGEVFFSPGIPLIRLQDIRFPEPYLAAFDGPRFGIAGVRERLQAF....RPIFFGVIKPNIGLPPQPFAELGYQSWTGLDIAKDDEMLADVDWCPLAERAALLGDACRRASAETGVPKIYLANITDE.VDRLTELHDVAVAN..........ALLIN.AMPVLSAVRMLRKHA.TVPLIAHFPFIAAFSR...NYGIHSRVMTRLQRLAGFDVVI..............VLDCIRACLE...........MGPIKPCLPVPGGSDSAATLENVYRKVGSADFGFVPGRGVFGHPMGPAAGATSIRQAWDAIAAGIPVPDHAASHPELAAALRAF................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE-LIKE PROTEIN 2]
2V67-A  : ....LTYYTPDYVV......DTDILAAFRMTPQ.....EECGAAVAAESST...........SLDRYKGRCYDIEP............IAYVAYXIDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFVGXPHGIQVERDKLNKY....RGLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTXDDENVNSQPFMRWRDRFLFVAEAIYKAQAETGEVKGHYLNATAGTCEEMMKRAVXAKEL..........IIMHD.YLTGFTANTSLAIYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHLH..............ILGFVDLMRDDYVE..YFTQDWXSMPGVMPVASGGIHVWHMPALVEIF.GDDACLQFGGGTLGHPWGNAPGAAANRVALEACTQ...IRSACKWSPELAAACEVW................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN]
3NWR-A  : ....................EDTLEADYLIET......ARVADVMAGEQSSG............ARSRASVLRIEE............RITLSFPLANI.........NLPTLAATVAGNLYDLGEVTGVRLLSLRLPASYRARFELPRHGVAGTRALTDVK....RPMIGTIIKPNVGLSAAETAALVRELCEAVDFIXDDEVCANPAHAPLAERVRAVMSEVRRYRERSGRPVMVAFNITDD.LDAMRRHAELVERE..........CVMAS.INWCFSAIQSLRRTT.PLVLHAHRNGYGMMSR...ALGMSFQAYQTLWRLSGVDHMH..............VIESARDCATP...............AVLPAFSSGQWAGTVQATFDAVRSTDLLFMSGGGILAHPDGPAAGVTSVRQAWAAVQAGTPLPVYAEHMPELRRALAFF................... [: A RUBISCO-LIKE PROTEIN]
3QFW-B  : ......................RIVATYHIAS......EQRALALAIEQSVEC............NIVGRVEDVAE............AVRIGLAAATAP.......AEPGQLLNMLFGNSSIQPD...IALADVELPAHYLTAFGGPRVGLAGIRTLTGAQ....RALTASALKP.QGLSPAALASIAHQLALGVDLIKDDHGLADQAFSPFAERAAAVGKAVREANAARGGRTLYAPNISG.TLDDMRRQLGVIRDE..........AVLVA.PMIVVSNFHAIVKEAAGLVVVAHPAMAGAA........IAAPLLGRLFRLFGADATV..............CLALAQAARD...........FGKLNACIPTPAGGIMLQRVNELLRFYG.QDVMLLI..........LTEQASRFVNKVADYGQR....................................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE]
uniref90: ......................RIIVTYQVAA......AARAEALAIEQSVEC............EIVGRVEAIAP............SVRVSLASATAP.......AEPGQLLNMLFGNSSIQPD...VTLADVELPPAYPAAFGGPKLGISGLRAKLGAP....RALTGSALKP.QGLAPEALAGLAHRLALGVDLIKDDHGIADQAFSPFAARVPAVARAMREACAVRGAAMLYAPHVSG.SLDDMRRQLDIVRRE..........VVMLM.PMIVLANFHLIAKEAEGLIVLAHPSLAGAQ........IAPDLLGKLFRLLGADATI..............CRALADAARR...........WHDLKPCLPVPAGGIAIDRIKELLAFYG.TDVMLLI..........LTEHAARFTAEVASHGQ........................................ [uniref90|Q6N7T7 Ribulose bisphosphate carboxylase-like protein 1 n=2 Tax=Rhodopseudomonas palustris RepID=RBLL1_RHOPA]
2ZVI-A  : ......................ELLATYLLT.......EKKAEQIATGLTVG...........MQKHKGRVIKVEE............VITIAYPEINFSQ.......DIPALLTTVFGKLSL...DGKIKLIDLHFSEAFKRALPGPKFGVYGIRKLLGE.....RPLLMSIFKGVIGRDLSDIKEQLRQQALGVDLIKDDEIFFETGLAPFETRIAEGKQILKETYEQTGHKTLYAVNLTGR.TADLKDKARRAAEL..........ALLFN.VFAYLDVMQGLAED..PVPIMAHPAVSGAFTS...FYGFSHALLGKLNRYCGADFSL..............ALAIHEECVR.............AFNQTFAVPSAGIHPGMVPLLMRDF.GIDHIINAGGGVHGHPNGAQGGGRAFRAIIDAVLEAQPIDEKAEQCKDLKLALDKWGK................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE]
uniref90: ......................................HKQAKIIAVGQTAG...........LRQHLAEVIEIKT..............KIRFPEINVEN.......DLASLLTMIFGKYSM...AGAAKVIGVHLPESYGQR...PKFGITGIRKILNV.....RPLIMAIFKPALGLSAADHAVILKQVADALDIIKDDEILGDLETAPTLKRLEACRQVLEAIKQQTGRTVLYAVNVTGK.ADKLIEKARLLVKE..........ALLLN.VLTYFSVLEALAAD..NVPIFAHPAFAGAMCA...DTGLSYSVIGRFMAHGGVDAVL..............EKKIRDSLRS.............VF....PVPSAGIHPGIVPKAIADY.GDDVILNAGTGIMDHPNNPGAGVKAFFEALERVKTGQSFTLDTVPEGALKQALQKWG.................. [uniref90|B7KIK8 Ribulose-bisphosphate carboxylase n=1 Tax=Cyanothece sp. PCC 7424 RepID=B7KIK8_CYAP7]
2OEK-B  : ......................AVMATYLLHDE.....RKKAEGIALGLTIG...........LRKHKGEVVAIEE............IVKIAYPTVNFSA.......DLPALLVTTFGKLSLD...GEVRLLDLEFPDEWKRQFPGPRFGIDGIRDRVGVH....RPLLMSIFKGMIGRDLAYLTSELKKQALGVDLVXDDEILFDSELLPFEKRITEGKAALQEVYEQTGKRTLYAVNLTGK.TFALKDKAKRAAEL..........VLLFN.VFAYLDVLQALRED..AVPIMAHPAFSGAVTP...FYGVAPSLWGKLLRLAGADFVL..............ALGIARALTD.............PFARAFPVPSAGIHPGLVPLIIRDF.GLDTIVNAGGGIHGHPDGAIGGGRAFRAAIDAVLAGRPLRAAAAENEALQKAIDRWGV................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE ENOLASE]
uniref90: .......................VIATYRLAGG.....TKKAETIALGMTVG...........LQRHAGRVVSVDA............LIRIAYPLANLTP.......DLPSLLTATFGKLSMD...GKIRLLDLTLPPTFAAAFPGPKLGVEGIRERLGVH....RPLLMSIFKSCVGLTLAELAEGFFQQALGVDLIKDDEIFFNDTDAPFEQRLEACLQATERARRETGQTVLYAINLTGP.VHRLPEKARRAARL..........ALLIN.VLPYFDLLQRLAED..TVPLIAHPALAGALYP...DYGIAAPLLGTLMRLAGADLVL..............ALGLASRLTD.............PHRPTFPVPSAGIHPGLVPHMMDDF.GLDVVINAGGGIHGHPGGAAAGGRAFRAAIAAGVGGVPLEQAAAGSRDLRAALDQWG.................. [uniref90|D5MLU6 2,3-diketo-5-methylthiopentyl-1-phosphate enolase (DK-MTP-1-P enolase) n=1 Tax=NC10 bacterium 'Dutch sediment' RepID=D5MLU6_9BACT]
3FK4-A  : ......................GIIATYLIHDD.....EKKAEQIALGLTIG...........LKQHKGNVIHVEE............IIKIEYPLLNFSP.......DLPAILTTTFGKLSLD...GEVKLIDLTFSDELKKHFPGPKFGIDGIRNLLQVH....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENALTPLTKRIVSGKEVLQSVYETYGHKTLYAVNLTGR.TFDLKENAKRAVQA..........ILLFN.VFAYLDVLQSLAED..PVPIMAHPAVSGAYSA...LYGVSSPLLGKLLRYAGADFSL..............ALAISKYLTE...........DASFKKSFSVPSAGIHPGFVPFIVRDF.GKDVVINAGGGIHGHPNGAQGGGKAFRTAIDATLQNKPLHEV..DDINLHSALQIWG.................. [: RUBISCO-LIKE PROTEIN]
uniref90: ......................GIIATYLIHDD.....EKKAEQIALGLTIG...........LKQHKGNVLHVEE............IIKIEYPLLNFSP.......DLPAILTTTFGKLSLD...GEVKLIDLTFSDELKKHFPGPKFGIDGIRNLLQVH....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENALTPLTNRIVSGKEVLQSVYETYGHKTLYAVNVTGR.TFDLKENAKRAVQA..........ILLFN.VFAYLDVLQSLAED..PVPIMAHPAVSGAYSA...LYGISSPLLGKLLRYAGADFSL..............ALAISKYLTE...........DVFFKKSFSVPSAGIHPGFVPFIIRDF.GKDVVINAGGGIHGHPNGAQGGGKAFRTAIDATLQNKPLHEV..DDINLHSALQIWG.................. [uniref90|C3P745 2,3-diketo-5-methylthiopentyl-1-phosphate enolase n=71 Tax=Bacillus cereus group RepID=MTNW_BACAA]

NOTE: To save space, only 20 of 1110 template profile alignments are shown above. The complete set of alignments can be found in the file Homology_5hjx-~_profile.ali. The template profile contains structural alignments of 16 PDB files, which provide safe anchors for the remaining sequence-based alignments (only reliable regions shown).

In the alignment above, 448 of 470 target residues (95.3%) are aligned to template residues. Among these aligned residues, the sequence identity is 64.5% and the sequence similarity is 75.9% ('similar' means that the BLOSUM62 score is > 0). The following 6 loops had to be modeled (only the first of 2 similar loops in the homodimer is listed):

LoopN-terminal anchorLoop sequenceC-terminal anchor
1VDGFVTGPAGVT
3VAFLVDGFVTGP
5KLIPAKGHGFLEV
7ETFAKYNSASHVAF
9EIDETAFGDDPVKGGGLFKV
11WREKLGVHKNone

After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).

The resulting half-refined model has been saved as Homology_5hjx-~03_refined050.yob and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals-0.259Good
Packing 1D-0.733Good
Packing 3D-1.305Satisfactory
Overall-0.930Good

Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as Homology_5hjx-~03_refined100.yob, the corresponding Z-scores are listed below:

Check typeQuality Z-scoreComment
Dihedrals0.188Optimal
Packing 1D-0.508Good
Packing 3D-1.449Satisfactory
Overall-0.844Good

Since the overall quality Z-score improved to -0.844 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.

NOTE: 8 residues contained in N- and C-terminal unaligned tails of the homodimeric model have been excluded from the Z-scores in both tables above, since they are not reliable (YASARA does not yet perform ab initio structure prediction) and would have mainly added noise to the result.

The final model for this template and alignment has been saved as Homology_5hjx-~03.yob, and is shown below, together with a plot of its overall quality Z-score, shown per residue:

6.15. Homology model 15/15, based on template 5HJX-~, alignment variant 04

This model is a homodimer, and based on the following profile-profile alignment:

(To improve readability, only up to ten lines of the complete target multiple sequence alignment (MSA) shown above are also displayed here (upside down). The template MSA has been shrunk and focused on structurally aligned PDB entries. The actual target-template alignment can be found in the middle at the line named 'Match'.)

Q08EW6  : .......................................................................................................................NNQGGGDIEHAKIHGIYMPERAIQLFDGPSKDISDMWRILGRPVKDGGYNAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEIQGNQVFSPMNQTIPLVVDAMKRAQDETGQAKLFSANITADDQYEMCARADFILEAFGP..DADKVAFLVDGYVGDPGMITTARSQYPNQYLHYHRAGHGAVNSPKIKRGYTAFVLAKMSRLQGASGAHVGTMGYGKME................................................................................................................................ [uniref90|Q08EW6 Ribulose 1,5-bisphosphate carboxylase/oxygenase large subunit (Fragment) n=1 Tax=uncultured marine bacterium RepID=Q08EW6_9BACT]
Q5DVV5  : ............................................................................................................................................................................IIKPKLGLRPKPFAEACYNFWLGGDFIKNDEPQGNQIWGPIKEVVPLVKDSLVRAQDDTGMAKLFSFNITADDHYEMLHRGEYILETFAEFSE..NIAFLVDGCVGGPGMVTTARRNFPDQFLHYHRAGHGAVTSDQSDRGYNMLVHMKMARLQGASGIHTGTMGYGKMEGAADDKVIAYMLERDSADGLSYHQEWEGMKATTPIICGGMNA...................................................................................... [uniref90|Q5DVV5 Ribulose-1,5-bisphosphate carboxylase oxygenase large subunit (Fragment) n=11 Tax=uncultured prokaryote RepID=Q5DVV5_9ZZZZ]
Q933G7  : ........................................................................................................................................VPPAYLRLFDGPSTTIKDLWRVLGRPVVDGGFIVGTIIKPKLGLRPQPFADACYDFWLGGDFIKNDEPQGNQVFAPFKDTVRAVNDAMRRAQDATGQPKLFSFNITADDHYEMLARGEYILETFGE..NADHVAFLVDGYVAGPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHVGTMGYGKMEGEASDRDSAFMITQDSAEGPYFKQEW...................................................................................................... [uniref90|Q933G7 Form II ribulose 1,5-bisphosphate carboxylase/oxygenase (Fragment) n=5 Tax=Rhodopseudomonas palustris RepID=Q933G7_RHOPA]
F2ZCE9  : .....................................................................................................................................DFYVPPDFLRLFDGPATTISNLWRVLGRPHQNGGFIVGTIVKPKLGLRPRPFADACYDFWLGGDFIKNDEPQGNQTFSPLKETIPLVADAMRRAQDETGEAKLFSANITADDHYEMVARGEFILDTFGEF..ADHVAFLVDGYVAGAAAVTTARRSFPQQYLHYHRAGHGAITSPQSKRGYTAFVHCKMARLQGASGIHTGTMSFGKMEGEAADRAIAFMLEQDSADGPYFHQEWHGMNPTTSIISG.......................................................................................... [uniref90|F2ZCE9 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=1 Tax=uncultured bacterium RepID=F2ZCE9_9BACT]
F2ZCD0  : ......................................................................................................................GNNQGMGDIANAQMQDFYVPPAMLALFDGPAKSINDLWTLLGRDNENGGYIAGTIIKPKLGLRPEPFAEAAYQFWLGGDFIKNDEPQGNQVFCPLKKVLPLVHDAMKRAQDETGEAKLFSLNITADDHYEMCARADFGLETFGE..DAPRLAFLVDGFVGGPGMVTTARRQYSSQYLHYHRAGHGMITSPSSKRGYTAYILAKMSRLMGASGIHVGTMGYGKMEGGADDKIIAYMIERDECQGPFYYQKWHGMKPTTPIVSGGM........................................................................................ [uniref90|F2ZCD0 Putative ribulose-1,5-bisphosphate carboxylase oxygenase form II (Fragment) n=4 Tax=uncultured bacterium RepID=F2ZCD0_9BACT]
F5BZE6  : ......................................................................................................................GNNQGMGDVEYAKMIDFYMARSLLTLFDGPAMNITDMWRVLGRPQVNGGMVVGTIIKPKLGLRPKPFADACYMFWMGGDFIKNDEPQGNQVFAPTREIIPLVAEAMERAQQETGEAKIFSANITADDPFEMIRRGEFILEAFGK..NASHVAFLVDGYVGGPSAVTLCRRYFPNQFLHYHRAGHGAVTSNQSKRGYTVLTHMKMSRLQGASGIHTGTMGYGKMEGDKNEKMVAYMIERDEAMGVYYNQPWHGMTATTPIISGGMNALR.................................................................................... [uniref90|F5BZE6 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II (Fragment) n=1 Tax=alpha proteobacterium LM-5 RepID=F5BZE6_9PROT]
Q9FPW1  : LDQSSRYADLSLDEATLVKNGKHVLVAYIMKPKAGYDYLATAAHFAAESSTGTNVNVCTTDDFTKSVDALVYYIDPDSEE.........MKIAYPTLLFDRNIIDGRGMMCSFLTLAIGNNQGMGDVEYGKIYDFYLPPSFLRLYDGPAVNVEDMWRILGKGTSNGGLVDGTIIKPKLGLQPNPFGEACYSFWQGGDFIKNDEPQGNQVFCQMNECIPEVVKAMRACVKETGSSKLFSANITADDPEEMIARGKYIMSQFGPLSE..NCAFLVDGYVAGGTAVTCCRRNFPKQFLHYHRAGHGSVTSPQTQRGYTAFVHTKISRVIGASGIHVGTMSFGKMEGDASDKNIAYMLQDDEADGPYYRQEWQGMKETTPIISGGMNALRLPAFFENLGHSNVILTAGGGSFGHKDGPKIGAISCRQGEEAWKSLSDVIEYAKTHEEIKGAFLTFQKDADQIYPGWKEKLG... [uniref90|Q9FPW1 Ribulose 1,5-bisphosphate carboxylase oxygenase large subunit n=1 Tax=Symbiodinium sp. RepID=Q9FPW1_SYMSP]
E6VVI6  : .DQTSRYVNFDLKEDQLIADGNHVLCAYIYKPANGYGNVEVAAHFAAESSTGTNVEVCTTDDFTKGVDALVYEVSDASNGDS......LMKIAYPVELFDRNIIDGRAMLASFLTLCIGNNQGMGDVAYAKMHDFYVPRQYLELFDGPSKNIADFWRMLGRPTENGGMIAGTIVKPKLGLRPKPFADACYHFWLGGDFVKNDEPQGNQVFAPLKETITAVADAMRRAQDETGEAKIFSANITADDPREMIARGEFILNAFGE..NASRVAFLVDGYVAGPTAITTARRNFPNQFLHYHRAGHGAVTSPQAKRGYTAFVLSKMSRLQGASGIHTGTMGFGKMEGEMADKSMAYMIEREEAQGPYFKQKWYGMKATTPMISGGMNALRLPGFFDNLGHSNICQTSGGGAFGHLDGPTAGALSLRQSHDAWIQGVNLLDYAKEHNELARAFESFPGDADRFYPTWRHQL.... [uniref90|E6VVI6 Ribulose-bisphosphate carboxylase n=1 Tax=Desulfovibrio aespoeensis Aspo-2 RepID=E6VVI6_DESAO]
Q8RTI1  : MDQSNRYADLSLKEDDLIKGGNHVLVAYLMKPKTGYGYLEAAAHFSAESSTGTNVEVSTTDDFTKGVDALVYEIDEAK.........EIMKIAYPVDLFDRNITDGRAMIVSFLTLAIGNNQGMGDIAYAKMLDFYVPQKYLRLFDGPSKDISDLWRILGRPVVNGGYIAGTIIKPKLGLRPKPFAEAAYQFWLGGDFIKNDEPQGNQVFSPMRETIPLVYDSMKRAMDETGEAKLFSANITADDHYEMMARGEFILNTFGP..DADKVAFLVDGYVGGPGMVTTARRHFANQYLHYHRAGHGAVTSPSAKRGYTAFVLAKMSRLQGASGIHVGTMGYGKMEGDATDKNIAYMIERDSADGPFYHQEWYGMKPTTPIISGGMNALRLPGFFENLGHANLINTSGGGSYGHIDSPAAGAISLRQAYECWQQGADPIEFAKEHKEFARAFESFPGDADTIFPGWREKLGVHK [uniref90|Q8RTI1 Ribulose-1,5-bisphosphate carboxylase/oxygenase form II n=1 Tax=magnetite-containing magnetic vibrio RepID=Q8RTI1_9PROT]
Q0F2Z8  : MDQSNRYADLSLNEADLIAGGKHLLVAYKLIPAKGYGFLEVAAHIAAESSTGTNVEVSTTDDFTRGVDALVYDIDETAFGDEGVTGGGLMKVAYPVELFDPNLIDGHYNVSHMWSLILGNNQGMGDHEGLRMLDFMVPECMIRKFDGPSAGIADLWKVLGRPEVDGGYISGTIIKPKLGLRPEPFAKACLDFWLGGDFIKNDEPQANQPFCPMKVVIPKVAEAMDRAQQETGQAKLFSANATADYHGECVARGEYILSEFAKYGNEKHVAFLIDGFVTGPAGVTTARRAFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLARLQGASGIHTGTMGYGKMEGHGKETVLAYMLERDECMGHYFNQKWYGMKPTAPIISGGMNALRLPGFFENLGHGNVINTCGGGSFGHIDSPAAGGKSLDQAYDCWKSGTDPIEYAKTHGEFARAFESFPGDADKLYPGWRDKLGVHK [uniref90|Q0F2Z8 Ribulose-bisphosphate carboxylase n=1 Tax=Mariprofundus ferrooxydans PV-1 RepID=Q0F2Z8_9PROT]
SecStr  : CCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEECCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCEEEECCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCEEECCCCCCHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCEEEECCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCHHHHHHHHHHHHHHHCCCCCCCCCCEEEECCCCCCHHHHHHHHHCCCCEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCHHCCCCCCCEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCHHHHHHCCHHHHHHHHHCCHHHHHHHHHHHHHHCCCC [Secondary structure predicted by PsiPred]
Target  : MDQSNRYANLNLKEEDLIKNGKHLLVAYKLIPAKGHGFLEVAAHVAAESSTGTNVEVSTTDDFTRGVDALVYEIDETAFGDDPVKGGGLFKVAYPVELFDPNLTDGTYNISHMWSLILGNNQGMGDHQGLRMLDFLVPEMMVRKFDGPSANISNLWKVLGRSETDGGYIAGTIIKPKLGLRPEPFAKACYDFWLGGDFIKNDEPQANQPFCPMEVVMPKVAEAMDRAQQATGQAKLFSANITADYYKEMIHRGDFVLETFAKYNSASHVAFLVDGFVTGPAGVTTARREFPDTFLHFHRAGHGAVTSYKSPMGMDPLCYMKLVRLMGASGMHTGTMGYGKMEGHGKETVLAYMLERDECQGPYFYQKWYGMKATTPIISGGMNALRLPGFFQNLGHGNVINTCGGGAFGHIDSPAAGGISLGQAYDCWKSGSDPIEYAKTHKEFARAFESFPKDGDKLFAGWREKLGVHK
Match   : MDQS :    NLKE:|LI :G|H:L AY | P    :F||:AAH :AESSTGTNVEVSTTDDFTRGVDALVYE|DE:          :L:K|AYP|ELFD N: DG   I: : :L |GNNQGMGD |  |M DF VP   :| FDGPS::I::LW|VLGR   :GG|I:GTIIKPKLGLRP|PFA:ACYDFWLGGDFI:NDEPQ:NQ F:P:: ::  VA|AM RAQ: TG|AKLFS NITAD | EM| RG|F|LETFA   :A:H|AFLVDG|V:GPA:VTTARR FP  |LH|HRAGHGAVTS :S  G   :   K|:RL:GASG:HTGTMG|GKMEG:: | :|AYM| :D ::GPYF|Q:W GM: TTPIISGGMNALR|PGFF:NLGH:N:I T:GGGAFGH|D: AAG: SL QA :CWK:G:DP|E|AK H|EFARAFESFP:D:DKL| :WR KL    
Template: MDQS.NRY..NLKESELIAGGRHVLCAYIMKPK...NFIQTAAHFVAESSTGTNVEVSTTDDFTRGVDALVYEVDEA..........SLMKIAYPIELFDRNVIDGRAMIASFLTLTIGNNQGMGDVEYAKMYDFYVPPAYLKLFDGPSTTIKDLWRVLGRPVINGGFIVGTIIKPKLGLRPQPFANACYDFWLGGDFIXNDEPQGNQVFAPFKDTVRAVADAMRRAQDKTGEAKLFSFNITADDHYEMLARGEFILETFAD..NADHIAFLVDGYVAGPAAVTTARRAFPKQYLHYHRAGHGAVTSPQSKRGYTAFVLSKMARLQGASGIHTGTMGFGKMEGEAADRAIAYMITEDAADGPYFHQEWLGMNPTTPIISGGMNALRMPGFFDNLGHSNLIMTAGGGAFGHVDGGAAGAKSLRQAEQCWKQGADPVEFAKDHREFARAFESFPQDADKLYPNWRAKL....
SecStr  : CCHH.HHH..TTHHHHHHHHCCCEEEEEEEECC...HHHHHHHHHHHHCCCCCCCCTTTTHHHHHHCCCEEEEEETT..........EEEEEEETTTTCCCCCCCCCCCHHHHHHHHHGGGGCTTTTEEEEEEEEECHHHHHHCCCCCCCCHHHHHHHHHCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCEEEEETTTTCCTTTTHHHHHHHHHHHHHHHHHHHHHCCCEEEEEECCCHHHHHHHHHHHHHHHHHC..TTTEEEEEEHHHHHCHHHHHHHHHHHCCCEEEEETTTTCCCCTTTTCCCCHHHHHHHHHHHHHCEEEEECTTTTCCCCCTTTTHHHHHHHHCEEEECCCEEEEETTTCCCEEEECCCCCCCHHHHHHHHHHCCCEEEEEHHHHHHCCCHHHHHHHHHHHHHHHHHHCCHHHHHHCCHHHHHHHHHHCHHHHHHHHCTTTTCC.... [Secondary structure assigned by YASARA]
1RSC-G  : .....LTY..DYTP.....KDTDLLAAFRFSPQ.....DEAGAAIAAESST..........TDMDRYKGKCYHIEP............FAFIAYPLDLFEE.......SVTNILTSIVGNVFGFKAIRSLRLEDIRFPVALVKTFQGPPHGIQVERDLLNKY....RPMLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKSQAETGEIKGHYLNVTAPTCEEMMKRAEFAKEL..........IIMHDFLTAGFTANTTLAKWCRGVLLHIHRAMHAVIDR...NHGIHFRVLAKCLRLSGGDHLH..............TLGFVDLMREDHIEA.FFTQDWASMPGVLPVASGGIHVWHMPALVEIF.GDDSVLQFGGGTLGHPWGNAPGATANRVALEACVQ...LREAGKWSPELAAALDLW................... [: RIBULOSE 1,5 BISPHOSPHATE CARBOXYLASE/OXYGENASE (LARGE]
1GEH-B  : ..........GYEP.......RDIIAVFRVTPA.....EQAAGAVAAESST.GTWT..YEQERWADLSAKAYDFHD............IVRIAYPFHAFEE.......NLPGLLASIAGNIFGMKRVKGLRLEDLYFPEKLIREFDGPAFGIEGVRKMLEIK....RPIYGVVPKPKVGYSPEEFEKLAYDLLSNADYMKDDENLTSPWYNRFEERAEIMAKIIDKVENETGEKKTWFANITAD.LLEMEQRLEVLADL..........HAMVDVVITGWGALRYIRDLAAGLAIHGHRAMHAAFTR...YHGISMFVLAKLYRLIGIDQLH..............VIQNARILRESHYK...LEQKFYSIKAAFPTSSGGLHPGNIQPVIEAL.GTDIVLQLGGGTLGHPDGPAAGARAVRQAIDAIMQGIPLDEYAKTHKELARALEKW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE]
1SVD-A  : ......TY..EYTP.....LDSDILACFKITPQ.....EEAAAAVAAESSTG..........DMDYYKGRAYRIED............YAFIAYPIDLFEE.......SVVNVFTSLVGNVFGFKAVRGLRLEDVRFPLAYVKTCGGPPHGIQVERDKMNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFMRWRDRFLFVQDATETAEAQTGERKGHYLNVTAPTPEEMYKRAEFAKEI..........IIMHDYITGGFTANTGLAKWCQGVLLHIHRAMHAVIDR...NHGIHFRVLTKILRLSGGDHLH..............TLGWIDLLRESFIP..FFDQDWGSMPGVFAVASGGIHVWHMPALVNIF.GDDSVLQFGGGTLGHPWGNAAGAAANRVALEACVE...LTAAAQHSPELKIAMETW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE]
2YBV-A  : .......Y..DYTP.....KDTDILAAFRVTPQ.....EEAAAAVAAESSTG........LTDLDRYKGCCYDIEP............IAYIAYPLDLFEE.......SVTNMLTSIVGNVFGFKALKALRLEDLRIPVAYLKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENINSQPFQRWRDRFLFVADAIHKAQAETGEIKGHYLNVTAPTCEEMLKRAEFAKEL..........IIMHDFLTAGFTANTTLSKWCRGMLLHIHRAMHAVMDR...NHGIHFRVLAKCLRMSGGDHIH..............TLGFVDLLRENYIE..YFTQDWASMPGVMAVASGGIHVWHMPALVDIF.GDDAVLQFG.....HPWGNAPGATANRVALEACIQ...IREAARWSPELAAAC...................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN]
1BXN-C  : .....MGY..DYVP.....KDTDLLALFRITPQ.....VEAAAAVAGESST..WTV......ACDMYRAKAYRVDP............FCYVAYDLSLFEE.......SIANLTASIIGNVFSFKPIKAARLEDMRFPVAYVKTFAGPSTGIIVERERLDKF....RPLLGATTKPKLGLSGRNYGRVVYEGLKGLDFMKDDENINSQPFMHWRDRFLFVMDAVNKASAATGEVKGSYLNVTAGTMEEMYRRAEFAKSL..........IIMVD.LIVGWTCIQSMSNWCRDMILHLHRAGHGTYTR...NHGVSFRVIAKWLRLAGVDHMH..............VQGYYNVCRDAYTQ..FFDQDWASLRKVMPVASGGIHAGQMHQLIHLF.GDDVVLQFGGGTIGHPQGIQAGATANRVALEAMVL...LRDAARWCGPLRAALDTW................... [: PROTEIN (RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN)]
1EJ7-L  : ......TY..EYQT.....KDTDILAAFRVTPQ.....EEAGAAVAAESSTGTWTTV.....SLDRYKGRCYRIER............IAYVAYPLDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFQGPPHGIQVERDKLNKY....RPLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTKDDENVNSQPFMRWRDRFLFCAEALYKAQAETGEIKGHYLNATAGTCEEMIKRAVFAREL..........IVMHDYLTGGFTANTSLAHYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHIH..............TLGFVDLLRDDFVE..YFTQDWVSLPGVLPVASGGIHVWHMPALTEIF.GDDSVLQFGGGTLGHPWGNAPGAVANRVALEACVK...IREACKWSPELAAACEVW................... [: RUBISCO (LARGE SUBUNIT)]
1IWA-C  : .....MGY..DYQV.....KDTDVLALFRVTPQ.....IEAAAAVAGESST...........AADLYRAKAYKVDQ............FAYIAYELDLFEE.......SIANLTASIIGNVFGFKAVKALRLEDMRLPLAYLKTFQGPATGVILERERLDKF....RPLLGCTTKPKLGLSGKNYGRVVYEALKGLDFVKDDENINSQPFMRWRERYLFTMEAVNKASAATGEVKGHYLNVTAATMEEMYARANFAKEL..........IIMID.LVIGYTAIQTMAKWARDMILHLHRAGNSTYSR...NHGMNFRVICKWMRMAGVDHIH..............TRGFYKTLLLPKLE..FFDMEWASLRKVMPVASGGIHAGQMHQLIHYLG.EDVVLQFGGGTIGHPDGIQAGATANRVALEAMIL...LREAAKTCGALRTALDLW................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE]
1TEL-B  : ......GF.............QYLVLDYYLESV.....ETALAHFCSEQSTA........DEDFRVHAAKVIDYEV............RVTIAHPHCNFGP.......KIPNLLTAVCGETYFTPGVPVVKLMDIHFPDTYLADFEGPKFGIEGLRDILNAH....RPIFFGVVKPNIGLSPGEFAEIAYQSWLGLDIAKDDEMLADVTWSSIEERAAHLGKARRKAEAETGEPKIYLANITDE.VDSLMEKHDVAVRN..........ALLINALPVGLSAVRMLSNYT.QVPLIGHFPFIASFSR...KYGIHSKVMTKLQRLAGLDAVI..............VLENVIECTKP..........MGRIKPCLPVPGGSDSALTLQTVYEKVGNVDFGFVPGRGVFGHPMGPKAGAKSIRQAWEAIEQGISIETWAETHPELQAMVDQ.................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE, LARGE SUBUNIT]
2D69-A  : ......DF..NYEP.....GRDELIVEYYFEPN.....EEAAGRIASESSIGTW.........AKRSMAKVFYLEK............IAKIAYPLTLFEE.......SLVQLFSAVAGNVFGMKALKNLRLLDFHPPYEYLRHFKGPQFGVQGIREFMGVK....RPLTATVPKPKMGWSVEEYAEIAYELWSGIDLLKDDENFTSFPFNRFEERVRKLYRVRDRVEAETGETKEYLINITGP.VNIMEKRAEMVANE..........YVMIDIVVAGWSALQYMREVTEGLAIHAHRAMHAAFTR...RHGITMLALAKAARMIGVDQIH..............IKRINDFLLS...........WEHIRPVFPVASGGLHPGLMPELIRLF.GKDLVIQAGGGVMGHPDGPRAGAKALRDAIDAAIEGVDLDEKAKSSPELKKSLREV................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE]
2QYG-D  : ......GF.............NYIELDFDFECA.....HEAAAHLCSEQSTA...........RPRFAAKVLELSA............RVTIAHPHGNF........AKIPNLLSAVCGEVFFSPGIPLIRLQDIRFPEPYLAAFDGPRFGIAGVRERLQAF....RPIFFGVIKPNIGLPPQPFAELGYQSWTGLDIAKDDEMLADVDWCPLAERAALLGDACRRASAETGVPKIYLANITDE.VDRLTELHDVAVAN..........ALLINAMPVGLSAVRMLRKHA.TVPLIAHFPFIAAFSR...NYGIHSRVMTRLQRLAGFDVVI..............VLDCIRACLE...........MGPIKPCLPVPGGSDSAATLENVYRKVGSADFGFVPGRGVFGHPMGPAAGATSIRQAWDAIAAGIPVPDHAASHPELAAALRAF................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE-LIKE PROTEIN 2]
2V67-A  : .....LTY..DYVV......DTDILAAFRMTPQ.....EECGAAVAAESST...........SLDRYKGRCYDIEP............IAYVAYXIDLFEE.......SVTNMFTSIVGNVFGFKALRALRLEDLRIPPAYVKTFVGXPHGIQVERDKLNKY....RGLLGCTIKPKLGLSAKNYGRAVYECLRGLDFTXDDENVNSQPFMRWRDRFLFVAEAIYKAQAETGEVKGHYLNATAGTCEEMMKRAVXAKEL..........IIMHDYLTGGFTANTSLAIYCRGLLLHIHRAMHAVIDR...NHGIHFRVLAKALRMSGGDHLH..............ILGFVDLMRDDYVE..YFTQDWXSMPGVMPVASGGIHVWHMPALVEIF.GDDACLQFGGGTLGHPWGNAPGAAANRVALEACTQ...IRSACKWSPELAAACEVW................... [: RIBULOSE BISPHOSPHATE CARBOXYLASE LARGE CHAIN]
3NWR-A  : ....................EDTLEADYLIET......ARVADVMAGEQSSG............ARSRASVLRIEE............RITLSFPLANI.........NLPTLAATVAGNLYDLGEVTGVRLLSLRLPASYRARFELPRHGVAGTRALTDVK....RPMIGTIIKPNVGLSAAETAALVRELCEAVDFIXDDEVCANPAHAPLAERVRAVMSEVRRYRERSGRPVMVAFNITDD.LDAMRRHAELVERE..........CVMASINWCGFSAIQSLRRTT.PLVLHAHRNGYGMMSR...ALGMSFQAYQTLWRLSGVDHMH..............VIESARDCATP...............AVLPAFSSGQWAGTVQATFDAVRSTDLLFMSGGGILAHPDGPAAGVTSVRQAWAAVQAGTPLPVYAEHMPELRRALAFF................... [: A RUBISCO-LIKE PROTEIN]
3QFW-B  : ......................RIVATYHIAS......EQRALALAIEQSVEC............NIVGRVEDVAE............AVRIGLAAATAP.......AEPGQLLNMLFGNSSIQPD...IALADVELPAHYLTAFGGPRVGLAGIRTLTGAQ....RALTASALKP.QGLSPAALASIAHQLALGVDLIKDDHGLADQAFSPFAERAAAVGKAVREANAARGGRTLYAPNISG.TLDDMRRQLGVIRDE..........AVLVAPMIVGVSNFHAIVKEAAGLVVVAHPAMAGAA........IAAPLLGRLFRLFGADATV..............CLALAQAARD...........FGKLNACIPTPAGGIMLQRVNELLRFYG.QDVMLLI..........LTEQASRFVNKVADYGQR....................................... [: RIBULOSE-1,5-BISPHOSPHATE CARBOXYLASE/OXYGENASE LARGE]
uniref90: ......................RIIVTYQVAA......AARAEALAIEQSVEC............EIVGRVEAIAP............SVRVSLASATAP.......AEPGQLLNMLFGNSSIQPD...VTLADVELPPAYPAAFGGPKLGISGLRAKLGAP....RALTGSALKP.QGLAPEALAGLAHRLALGVDLIKDDHGIADQAFSPFAARVPAVARAMREACAVRGAAMLYAPHVSG.SLDDMRRQLDIVRRE..........VVMLMPMIVGLANFHLIAKEAEGLIVLAHPSLAGAQ........IAPDLLGKLFRLLGADATI..............CRALADAARR...........WHDLKPCLPVPAGGIAIDRIKELLAFYG.TDVMLLI..........LTEHAARFTAEVASHGQ........................................ [uniref90|Q6N7T7 Ribulose bisphosphate carboxylase-like protein 1 n=2 Tax=Rhodopseudomonas palustris RepID=RBLL1_RHOPA]
2ZVI-A  : ......................ELLATYLLT.......EKKAEQIATGLTVG...........MQKHKGRVIKVEE............VITIAYPEINFSQ.......DIPALLTTVFGKLSL...DGKIKLIDLHFSEAFKRALPGPKFGVYGIRKLLGE.....RPLLMSIFKGVIGRDLSDIKEQLRQQALGVDLIKDDEIFFETGLAPFETRIAEGKQILKETYEQTGHKTLYAVNLTGR.TADLKDKARRAAEL..........ALLFNVFAYGLDVMQGLAED..PVPIMAHPAVSGAFTS...FYGFSHALLGKLNRYCGADFSL..............ALAIHEECVR.............AFNQTFAVPSAGIHPGMVPLLMRDF.GIDHIINAGGGVHGHPNGAQGGGRAFRAIIDAVLEAQPIDEKAEQCKDLKLALDKWGK................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE]
uniref90: ......................................HKQAKIIAVGQTAG...........LRQHLAEVIEIKT..............KIRFPEINVEN.......DLASLLTMIFGKYSM...AGAAKVIGVHLPESYGQR...PKFGITGIRKILNV.....RPLIMAIFKPALGLSAADHAVILKQVADALDIIKDDEILGDLETAPTLKRLEACRQVLEAIKQQTGRTVLYAVNVTGK.ADKLIEKARLLVKE..........ALLLNVLTYGFSVLEALAAD..NVPIFAHPAFAGAMCA...DTGLSYSVIGRFMAHGGVDAVL..............EKKIRDSLRS.............VF....PVPSAGIHPGIVPKAIADY.GDDVILNAGTGIMDHPNNPGAGVKAFFEALERVKTGQSFTLDTVPEGALKQALQKWG.................. [uniref90|B7KIK8 Ribulose-bisphosphate carboxylase n=1 Tax=Cyanothece sp. PCC 7424 RepID=B7KIK8_CYAP7]
2OEK-B  : ......................AVMATYLLHDE.....RKKAEGIALGLTIG...........LRKHKGEVVAIEE............IVKIAYPTVNFSA.......DLPALLVTTFGKLSLD...GEVRLLDLEFPDEWKRQFPGPRFGIDGIRDRVGVH....RPLLMSIFKGMIGRDLAYLTSELKKQALGVDLVXDDEILFDSELLPFEKRITEGKAALQEVYEQTGKRTLYAVNLTGK.TFALKDKAKRAAEL..........VLLFNVFAYGLDVLQALRED..AVPIMAHPAFSGAVTP...FYGVAPSLWGKLLRLAGADFVL..............ALGIARALTD.............PFARAFPVPSAGIHPGLVPLIIRDF.GLDTIVNAGGGIHGHPDGAIGGGRAFRAAIDAVLAGRPLRAAAAENEALQKAIDRWGV................. [: 2,3-DIKETO-5-METHYLTHIOPENTYL-1-PHOSPHATE ENOLASE]
uniref90: .......................VIATYRLAGG.....TKKAETIALGMTVG...........LQRHAGRVVSVDA............LIRIAYPLANLTP.......DLPSLLTATFGKLSMD...GKIRLLDLTLPPTFAAAFPGPKLGVEGIRERLGVH....RPLLMSIFKSCVGLTLAELAEGFFQQALGVDLIKDDEIFFNDTDAPFEQRLEACLQATERARRETGQTVLYAINLTGP.VHRLPEKARRAARL..........ALLINVLPYGFDLLQRLAED..TVPLIAHPALAGALYP...DYGIAAPLLGTLMRLAGADLVL..............ALGLASRLTD.............PHRPTFPVPSAGIHPGLVPHMMDDF.GLDVVINAGGGIHGHPGGAAAGGRAFRAAIAAGVGGVPLEQAAAGSRDLRAALDQWG.................. [uniref90|D5MLU6 2,3-diketo-5-methylthiopentyl-1-phosphate enolase (DK-MTP-1-P enolase) n=1 Tax=NC10 bacterium 'Dutch sediment' RepID=D5MLU6_9BACT]
3FK4-A  : ......................GIIATYLIHDD.....EKKAEQIALGLTIG...........LKQHKGNVIHVEE............IIKIEYPLLNFSP.......DLPAILTTTFGKLSLD...GEVKLIDLTFSDELKKHFPGPKFGIDGIRNLLQVH....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENALTPLTKRIVSGKEVLQSVYETYGHKTLYAVNLTGR.TFDLKENAKRAVQA..........ILLFNVFAYGLDVLQSLAED..PVPIMAHPAVSGAYSA...LYGVSSPLLGKLLRYAGADFSL..............ALAISKYLTE...........DASFKKSFSVPSAGIHPGFVPFIVRDF.GKDVVINAGGGIHGHPNGAQGGGKAFRTAIDATLQNKPLHEV..DDINLHSALQIWG.................. [: RUBISCO-LIKE PROTEIN]
uniref90: ......................GIIATYLIHDD.....EKKAEQIALGLTIG...........LKQHKGNVLHVEE............IIKIEYPLLNFSP.......DLPAILTTTFGKLSLD...GEVKLIDLTFSDELKKHFPGPKFGIDGIRNLLQVH....RPLLMSIFKGMIGRNIGYLKTQLRDQAIGVDIVKDDEILFENALTPLTNRIVSGKEVLQSVYETYGHKTLYAVNVTGR.TFDLKENAKRAVQA..........ILLFNVFAYGLDVLQSLAED..PVPIMAHPAVSGAYSA...LYGISSPLLGKLLRYAGADFSL..............ALAISKYLTE...........DVFFKKSFSVPSAGIHPGFVPFIIRDF.GKDVVINAGGGIHGHPNGAQGGGKAFRTAIDATLQNKPLHEV..DDINLHSALQIWG.................. [uniref90|C3P745 2,3-diketo-5-methylthiopentyl-1-phosphate enolase n=71 Tax=Bacillus cereus group RepID=MTNW_BACAA]

NOTE: To save space, only 20 of 1110 template profile alignments are shown above. The complete set of alignments can be found in the file Homology_5hjx-~_profile.ali. The template profile contains structural alignments of 16 PDB files, which provide safe anchors for the remaining sequence-based alignments (only reliable regions shown).

In the alignment above, 448 of 470 target residues (95.3%) are aligned to template residues. Among these aligned residues, the sequence identity is 64.1% and the sequence similarity is 75.9% ('similar' means that the BLOSUM62 score is > 0). The following 6 loops had to be modeled (only the first of 2 similar loops in the homodimer is listed):

LoopN-terminal anchorLoop sequenceC-terminal anchor
1MDQSNRYANL
3SNRYANLNLKEED
5LETFAKYNSASHV
7KLIPAKGHGFLEV
9EIDETAFGDDPVKGGGLFKV
11WREKLGVHKNone

After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).

The resulting half-refined model has been saved as Homology_5hjx-~04_refined050.yob and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals0.088Optimal
Packing 1D-0.791Good
Packing 3D-1.198Satisfactory
Overall-0.853Good

Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as Homology_5hjx-~04_refined100.yob, the corresponding Z-scores are listed below:

Check typeQuality Z-scoreComment
Dihedrals0.475Optimal
Packing 1D-0.432Good
Packing 3D-1.314Satisfactory
Overall-0.711Good

Since the overall quality Z-score improved to -0.711 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.

NOTE: 8 residues contained in N- and C-terminal unaligned tails of the homodimeric model have been excluded from the Z-scores in both tables above, since they are not reliable (YASARA does not yet perform ab initio structure prediction) and would have mainly added noise to the result.

The final model for this template and alignment has been saved as Homology_5hjx-~04.yob, and is shown below, together with a plot of its overall quality Z-score, shown per residue:

7. The model ranking

The following table lists the 15 models sorted by their overall quality Z-scores. The models have been superposed and saved together as Homology.sce.

RankZ-scoreStructureStateModel IDFilenameOriginal numberResiduesComment
1-0.380homodimer7T1C-~01Homology_7t1c-~01.yob12-467Good
2-0.514homodimer7T1C-~02Homology_7t1c-~02.yob22-467Good
3-0.630homodimer5HJX-~02Homology_5hjx-~02.yob131-466Good
4-0.663homodimer5HAN-~01Homology_5han-~01.yob81-466Good
5-0.677homodimer5HJX-~01Homology_5hjx-~01.yob121-466Good
6-0.686homodimer5C2C-~01Homology_5c2c-~01.yob33-470Good
7-0.711homodimer5HJX-~04Homology_5hjx-~04.yob151-466Good
8-0.728homodimer5HAN-~02Homology_5han-~02.yob91-466Good
9-0.731homodimer5HAN-~04Homology_5han-~04.yob111-466Good
10-0.783homodimer5HQM-~01Homology_5hqm-~01.yob51-470Good
11-0.807homodimer5C2C-~02Homology_5c2c-~02.yob43-470Good
12-0.812homodimer5HAN-~03Homology_5han-~03.yob101-466Good
13-0.844homodimer5HJX-~03Homology_5hjx-~03.yob141-466Good
14-0.844homodimer5HQM-~02Homology_5hqm-~02.yob61-470Good
15-0.863homodimer5HQM-~03Homology_5hqm-~03.yob71-470Good

8. The hybrid model

Finally, YASARA tried to combine the best parts of the 15 models to obtain a hybrid model, hoping to increase the accuracy beyond each of the contributors. The following fragments were copied from other models (note that the first transfer is simply the initial model considered most suitable for hybridization, and that the scores in the right column are not comparable to the Z-scores listed further above, since they now penalize missing and very exposed residues):

TransferFirst residueLast residueLengthFrom modelScore
1 1 470 470 5HJX-~02 -0.913
2 70 90 21 7T1C-~01 -0.863 accepted
3 464 470 7 5HQM-~02 -0.850 accepted
4 461 467 7 5C2C-~02 -0.845 accepted
5 32 39 8 7T1C-~01 -0.823 accepted
6 411 419 9 5C2C-~02 -0.824 rejected
7 357 370 14 7T1C-~01 -0.833 rejected
8 319 325 7 7T1C-~01 -0.835 rejected
9 461 464 4 5C2C-~02 -0.832 rejected
10 261 264 4 7T1C-~01 -0.820 accepted
11 355 369 15 7T1C-~01 -0.821 rejected
12 411 418 8 5C2C-~02 -0.810 accepted
13 356 369 14 7T1C-~01 -0.828 rejected
14 434 440 7 7T1C-~01 -0.791 accepted
15 316 325 10 7T1C-~02 -0.802 rejected
16 315 324 10 7T1C-~02 -0.788 accepted
17 357 370 14 7T1C-~01 -0.795 rejected
18 138 145 8 7T1C-~01 -0.775 accepted
19 462 465 4 5C2C-~02 -0.788 rejected
20 143 146 4 5HAN-~02 -0.783 rejected

The resulting hybrid model obtained the following quality Z-scores (this time the score includes floppy terminal tails):

Check typeQuality Z-scoreComment
Dihedrals0.467Optimal
Packing 1D0.293Optimal
Packing 3D-1.144Satisfactory
Overall-0.350Good

The following figure shows the initial model in blue, and all hybridized parts in a different color.

This hybrid model with Z-score -0.350 was saved as the final one, Homology.yob

NOTE: If the hybrid model scores worse than the model from which it was initially derived, this is not necessarily a bad thing, since the hybrid model often covers more residues.

NOTE: A Z-score describes how many standard deviations the model quality is away from the average high-resolution X-ray structure. Higher values are better, negative values indicate that the homology model looks worse than a high-resolution X-ray structure. The overall Z-scores for all models have been calculated as the weighted averages of the individual Z-scores using the formula Overall = 0.145*Dihedrals + 0.390*Packing1D + 0.465*Packing3D. The overall score thus captures the correctness of backbone- (Ramachandran plot) and side-chain dihedrals, as well as packing interactions. It applies to globular proteins only, and can be mislead by artificial structures like long single alpha helices (which have perfect dihedrals and are free of packing errors, since there is no packing).

Created Wed Dec 14 19:50:45 2022 by YASARA Structure.